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Kress J, Vermeulen M, Chudy M, Reissinger A, Hanschmann KM, Saville A, Nübling CM. Reliability of CE-marked NATs for HIV-1 subtype C detection and quantitation. J Clin Virol 2020; 132:104649. [PMID: 33027700 DOI: 10.1016/j.jcv.2020.104649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
We compared seven CE-marked HIV-1 RNA nucleic acid amplification technology (NAT) based assays for their detection efficiency and quantitation concordance in regard to HIV-1 subtype C. We used 398 plasma samples from South African repeat blood donors identified as HIV positive at occasion of routine screening NAT performed mainly during the years 2010-2013, with most plasma samples reflecting recent HIV-1 infections. All HIV-1 subtype C specimens were detected, independent of mono- or dual-target assay design. In the same time period new variants of HIV-1 subtype B had been identified which were missed by some mono-target assays, a finding which was not corroborated for subtype C in our study. A high level of concordance of HIV-1 subtype C quantitation was determined for the HIV-1 NATs, showing successful standardization in this diagnostic field.
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Affiliation(s)
- J Kress
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - M Vermeulen
- South African National Blood Service, Constantia Kloof, Johannesburg, South Africa
| | - M Chudy
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - A Reissinger
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - K-M Hanschmann
- Section of Biostatistics, Paul-Ehrlich-Institut, Langen, Germany
| | - A Saville
- South African National Blood Service, Constantia Kloof, Johannesburg, South Africa
| | - C M Nübling
- Division of Major Policy Issues, Coordination, Paul-Ehrlich-Institut, Langen, Germany.
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2
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Thirion L, Pezzi L, Corcostegui I, Dubot-Pérès A, Falchi A, de Lamballerie X, Charrel RN. Development and Evaluation of a Duo Chikungunya Virus Real-Time RT-PCR Assay Targeting Two Regions within the Genome. Viruses 2019; 11:v11080755. [PMID: 31443243 PMCID: PMC6722894 DOI: 10.3390/v11080755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Chikungunya virus (CHIKV) re-emerged as a globalized health threat fifteen years ago. There are dozens of RT-PCR assays published. An inventory of the latter was made, and after in silico analysis, two assays were selected for their ability to detect strains belonging to the five CHIKV genetic lineages. They were combined in order to provide a robust assay not affected by genetic point mutations and the resulting Duo CHIKV real-time RT-PCR assay was compared to the two parental single-plex tests against five strains belonging to the five genetic lineages. The Duo CHIKV assay performed equally, or better, in terms of sensitivity, specificity, linearity and signal intensity. Dual-target assays are better suited for viruses having the propensity to evolve into new variants via point mutations or major sequence deletions/insertions. Here, we demonstrated that combining two single systems into a dual-target assay did not impair sensitivity and specificity, and proved a potent diagnostic tool to face a potential emergence of CHIKV variants by newly evolving mutations.
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Affiliation(s)
- Laurence Thirion
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France
| | - Laura Pezzi
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 94925 Corte, France
| | - Iban Corcostegui
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France
| | - Audrey Dubot-Pérès
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse-Inserm, 94925 Corte, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France
| | - Remi N Charrel
- Unité des Virus Emergents (UVE: Aix Marseille Univ., IRD 190, INSERM 1207, IHU Méditerranée Infection), 13005 Marseille, France.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32601, USA.
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3
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Li Q, Liu Z, Zhou D, Pan J, Liu C, Chen J. A cascade toehold-mediated strand displacement strategy for label-free and sensitive non-enzymatic recycling amplification detection of the HIV-1 gene. Analyst 2019; 144:2173-2178. [PMID: 30768078 DOI: 10.1039/c8an02340a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In this work, a label-free fluorescence biosensor for simple detection of the HIV-1 gene was proposed by using toehold-mediated strand displacement reactions (TMSDRs) combined with a non-enzymatic target recycling amplification strategy. In this system, two TMSDRs were used. In the presence of the HIV-1 gene, an autocatalytic DNA machine can be activated. This leads to the generation of numerous free G-rich sequences, which can associate with a fluorescent dye N-methylmesoporphyrin IX (NMM) to yield an amplified fluorescence signal for the target detection. This sensing platform showed a high sensitivity towards the HIV-1 gene with a detection limit as low as 1.9 pM without any labelling, immobilization, or washing steps. The designed sensing system also exhibits an excellent selectivity for the HIV-1 gene compared with other interference DNA sequences. Furthermore, the presented biosensor is robust and has been successfully applied for the detection of the HIV-1 gene in a real biological sample with satisfactory results, suggesting that this method is promising for simple and early clinical diagnosis of HIV infection. Thanks to its simplicity, cost-effectiveness and ultrasensitivity, our proposed sensing strategy provides a universal platform for the detection of other genes by substituting the target-recognition element.
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Affiliation(s)
- Qiong Li
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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4
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Cascade toehold-mediated strand displacement along with non-enzymatic target recycling amplification for the electrochemical determination of the HIV-1 related gene. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2368-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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5
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Zolt SD, Thermann R, Bangsow T, Pichl L, Müller B, Jork C, Weber-Schehl M, Hedges D, Schupp I, Unverzagt P, de Rue K, Roth WK. Implementation of an HIV-1 Triple-Target NAT Assay in the Routine Screening at Three German Red Cross Blood Centres. Transfus Med Hemother 2016; 43:183-9. [PMID: 27403090 DOI: 10.1159/000446290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Blood product safety was significantly improved by the introduction of NAT testing in the late 1990s, resulting in a strong decrease of transfusion-transmitted infections (TTIs). Due to the occurrence of HIV-1 NAT test failures as a consequence of mismatch mutations in the amplicon regions of mono-target NAT assays, the Paul Ehrlich Institute mandated the implementation of multi-target NAT assays for HIV-1 in 2014. Commercial suppliers mostly developed dual-target NAT assays, with only one implementing a triple-target NAT assay. METHODS The HIV-1 triple-target NAT assay v3 (GFE Blut) was tested on mutated specimens and synthetic DNA bearing mutations that resulted in sample underquantification or false-negative test results. In addition, data from 2 years routine testing at three German Red Cross Blood centres were analysed. RESULTS The HIV-1 triple-target PCR could compensate for all mutations tested and could compensate the loss of one amplicon without a significant loss of sensitivity. Data from 2 years routine testing showed a solid performance. CONCLUSION The HIV-1 triple-target v3 assay (GFE Blut) can compensate mutations in target sequences better than a dual-target assay and is applicable to high-throughput screening, thus increasing blood product safety.
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Affiliation(s)
- Silke De Zolt
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Rolf Thermann
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Thorsten Bangsow
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Lutz Pichl
- DRK Blutspendedienst West, Hagen, Germany
| | | | | | | | - Doris Hedges
- Blutspendedienst des Bayerischen Roten Kreuzes, Wiesentheid, Germany
| | - Ingo Schupp
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Patrick Unverzagt
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - Katrin de Rue
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
| | - W Kurt Roth
- Gesellschaft zur Forschung, Entwicklung und Distribution von Diagnostika im Blutspendewesen mbH (GFE Blut), Frankfurt/M., Germany
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Amendola A, Pisciotta M, Aleo L, Ferraioli V, Angeletti C, Capobianchi MR. Evaluation of the Aptima(®) HIV-1 Quant Dx assay for HIV-1 RNA viral load detection and quantitation in plasma of HIV-1-infected individuals: A comparison with Abbott RealTime HIV-1 assay. J Med Virol 2016; 88:1535-44. [PMID: 26864171 PMCID: PMC6585778 DOI: 10.1002/jmv.24493] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2016] [Indexed: 11/16/2022]
Abstract
The Hologic Aptima® HIV‐1 Quant Dx assay (Aptima HIV) is a real‐time transcription‐mediated amplification method CE‐approved for use in diagnosis and monitoring of HIV‐1 infection. The analytical performance of this new assay was compared to the FDA‐approved Abbott RealTime HIV‐1 (RealTime). The evaluation was performed using 220 clinical plasma samples, the WHO 3rd HIV‐1 International Standard, and the QCMD HIV‐1 RNA EQA. Concordance on qualitative results, correlation between quantitative results, accuracy, and reproducibility of viral load data were analyzed. The ability to measure HIV‐1 subtypes was assessed on the second WHO International Reference Preparation Panel for HIV‐1 Subtypes. With clinical samples, inter‐assay agreement for qualitative results was high (91.8%) with Cohen's kappa statistic equal to 0.836. For samples with quantitative results in both assays (n = 93), Lin's concordance correlation coefficient was 0.980 (P
< 0.0001) and mean differences of measurement, conducted according to Bland–Altman method, was low (0.115 log10 copies/ml). The Aptima HIV quantified the WHO 3rd HIV‐1 International Standard diluted from 2000 to 31 cp/ml (5,700–88 IU/ml) at expected values with excellent linearity (R2 > 0.970) and showed higher sensitivity compared to RealTime being able to detect HIV‐1 RNA in 10 out of 10 replicates containing down to 7 cp/ml (20 IU/ml). Reproducibility was very high, even at low HIV‐1 RNA values. The Aptima HIV was able to detect and accurately quantify all the main HIV‐1 subtypes in both reference panels and clinical samples. Besides excellent performance, Aptima HIV shows full automation, ease of use, and improved workflow compared to RealTime. J. Med. Virol. 88:1535–1544, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Maria Pisciotta
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Loredana Aleo
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Valeria Ferraioli
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Claudio Angeletti
- Department of EpidemiologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
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7
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Shah K, Ragupathy V, Saga A, Hewlett I. High sensitivity detection of HIV-1 using two genomic targets compared with single target PCR. J Med Virol 2015; 88:1092-7. [PMID: 26575693 DOI: 10.1002/jmv.24431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2015] [Indexed: 11/10/2022]
Abstract
The genetic diversity of Human Immunodeficiency Virus type-1(HIV-1) has been shown to affect the performance of Nucleic Acid Testing (NAT) of Human Immunodeficiency Virus type-1. Although, majority NAT assays were designed to detect the conserved regions of HIV-1 mutations at the primer or probe binding regions may lead to false negatives. In this study, we evaluated the feasibility of detecting two genomic targets for enhanced sensitivity. A total of 180 tests using HIV-1 VQA RNA quantitation standard, 240 tests using EQAPOL HIV-1 viral diversity subtype panel, and 30 clinical plasma samples from Cameroon were evaluated. The analysis was based on probit and hit rate. The genomic targets LOD estimated by PROBIT for the gag target was 118 cps/ml (95%CI 64 cps/ml lower bound), Pol or POL/LTR was at 40 cps/ml (95%CI 17, 16 cps/ml), LTR 45 cps/ml (95%CI 20 cps/ml lower bound), and Gag/LTR at 67.8 cps/ml (95%CI 32 cps/ml lower bound). For HIV-1 subtypes the overall reactivity was 55-100% when tested at 100 and 1000 cps/ml and combination of genomic targets detection increased the reactivity to 100%. The plasma samples evaluation showed LTR or pol/LTR combination yielded higher sensitivity for patients with lower viral load (<40 cps/ml). We conclude that detection of two HIV-1 genomic targets improved sensitivity for detection of genetically diverse HIV-1 strains.
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Affiliation(s)
- Krishna Shah
- LMV/DETTD/OBRR/CBER/FDA, Bethesda, Maryland.,Voluntary Intern, Northwest High School, Germantown, Maryland
| | | | - Anusha Saga
- Summer Intern, Thomas Jefferson High School for Science and Technology, Alexandria, Virginia
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8
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Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Sci Rep 2015; 5:13201. [PMID: 26285800 PMCID: PMC4541070 DOI: 10.1038/srep13201] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 07/14/2015] [Indexed: 01/05/2023] Open
Abstract
Although nearly one fifth of all human cancers have an infectious aetiology, the causes for the majority of cancers remain unexplained. Despite the enormous data output from high-throughput shotgun sequencing, viral DNA in a clinical sample typically constitutes a proportion of host DNA that is too small to be detected. Sequence variation among virus genomes complicates application of sequence-specific, and highly sensitive, PCR methods. Therefore, we aimed to develop and characterize a method that permits sensitive detection of sequences despite considerable variation. We demonstrate that our low-stringency in-solution hybridization method enables detection of <100 viral copies. Furthermore, distantly related proviral sequences may be enriched by orders of magnitude, enabling discovery of hitherto unknown viral sequences by high-throughput sequencing. The sensitivity was sufficient to detect retroviral sequences in clinical samples. We used this method to conduct an investigation for novel retrovirus in samples from three cancer types. In accordance with recent studies our investigation revealed no retroviral infections in human B-cell lymphoma cells, cutaneous T-cell lymphoma or colorectal cancer biopsies. Nonetheless, our generally applicable method makes sensitive detection possible and permits sequencing of distantly related sequences from complex material.
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9
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Natural mannosylation of HIV-1 gp120 imposes no immunoregulatory effects in primary human plasmacytoid dendritic cells. Mol Immunol 2014; 59:180-7. [DOI: 10.1016/j.molimm.2014.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 02/09/2014] [Accepted: 02/11/2014] [Indexed: 01/15/2023]
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10
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Chudy M, Kress J, Halbauer J, Heiden M, Funk MB, Nübling CM. Risk Minimization Measures for Blood Screening HIV-1 Nucleic Acid Amplification Technique Assays in Germany. ACTA ACUST UNITED AC 2013; 41:45-51. [PMID: 24659947 DOI: 10.1159/000357103] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/16/2013] [Indexed: 11/19/2022]
Abstract
BACKGROUND Several publications describe HIV-1 RNA false-negative results or viral load underquantitation associated with Communauté Européenne(CE)-marked qualitative or quantitative nucleic acid amplification technique (NAT) assays. 6 cases occurred during blood screening in Germany, with 2 of them causing HIV-1 transmissions to recipients of blood components. The implicated NAT assays were mono-target assays amplifying in different viral genome regions (gag or long terminal repeat). METHODS Specimens characterized by HIV-1 NAT underquantitation or false-negative NAT results were comparatively investigated in CE-marked HIV-1 NAT systems of different design to identify potential reasons. The target regions of the viral nucleic acids were sequenced and these sequences compared to primers and probes of the assays. Potential risk minimization measures were considered for quantitative and blood-screening HIV-1 NAT systems. RESULTS Nucleotide sequencing of the viral target region in cases of HIV-1 RNA underquantitation or false-negative test results revealed new HIV-1 variants that were mismatched with primers and probes used in some mono-target assays. So far, dualtarget NAT assays have not been associated with mismatch-based false-negative test results. From 2015, the Paul Ehrlich Institute will request HIV-1 NAT assays of dual-target design or an analogous solution for further reducing the risk in blood screening. CONCLUSION HIV differs from other blood-borne viruses with regard to its fast evolution of new viral variants. The evolution of new sequences is hardly predictable; therefore, NAT assays with only 1 target region appear to be more vulnerable to sequence variations than dual-target assays. The associated risk may be higher for HIV-1 NAT assays used for blood screening compared to quantitative assays used for monitoring HIV-1-infected patients. In HIV-1 screening NAT assays of dual-target design may adequately address the risk imposed by new HIV-1 variants.
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Affiliation(s)
- Michael Chudy
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Julia Kress
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Jochen Halbauer
- Section of Hemovigilance and IVD Vigilance, Paul-Ehrlich-Institut, Langen, Germany
| | - Margarethe Heiden
- Section of Transfusion Medicine, Paul-Ehrlich-Institut, Langen, Germany
| | - Markus B Funk
- Section of Hemovigilance and IVD Vigilance, Paul-Ehrlich-Institut, Langen, Germany
| | - C Micha Nübling
- Section of Molecular Virology, Paul-Ehrlich-Institut, Langen, Germany
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11
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Molecular virology in transfusion medicine laboratory. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2012; 11:203-16. [PMID: 23356973 DOI: 10.2450/2012.0219-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Low cost HIV-1 quantitative RT-PCR assay in resource-limited settings: Improvement and implementation. J Virol Methods 2012; 185:118-23. [DOI: 10.1016/j.jviromet.2012.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 06/06/2012] [Accepted: 06/12/2012] [Indexed: 11/18/2022]
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13
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Manak M, Sina S, Anekella B, Hewlett I, Sanders-Buell E, Ragupathy V, Kim J, Vermeulen M, Stramer SL, Sabino E, Grabarczyk P, Michael N, Peel S, Garrett P, Tovanabutra S, Busch MP, Schito M. Pilot studies for development of an HIV subtype panel for surveillance of global diversity. AIDS Res Hum Retroviruses 2012; 28:594-606. [PMID: 22149143 DOI: 10.1089/aid.2011.0271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The continued global spread and evolution of HIV diversity pose significant challenges to diagnostics and vaccine strategies. NIAID partnered with the FDA, WRAIR, academia, and industry to form a Viral Panel Working Group to design and prepare a panel of well-characterized current and diverse HIV isolates. Plasma samples that had screened positive for HIV infection and had evidence of recently acquired infection were donated by blood centers in North and South America, Europe, and Africa. A total of 80 plasma samples were tested by quantitative nucleic acid tests, p24 antigen, EIA, and Western blot to assign a Fiebig stage indicative of approximate time from initial infection. Evaluation of viral load using FDA-cleared assays showed excellent concordance when subtype B virus was tested, but lower correlations for subtype C. Plasma samples were cocultivated with phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from normal donors to generate 30 viral isolates (50-80% success rate for samples with viral load >10,000 copies/ml), which were then expanded to 10(7)-10(9) virus copies per ml. Analysis of env sequences showed that sequences derived from cultured PBMCs were not distinguishable from those obtained from the original plasma. The pilot collection includes 30 isolates representing subtypes B, C, B/F, CRF04_cpx, and CRF02_AG. These studies will serve as a basis for the development of a comprehensive panel of highly characterized viral isolates that reflects the current dynamic and complex HIV epidemic, and will be made available through the External Quality Assurance Program Oversight Laboratory (EQAPOL).
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Affiliation(s)
- Mark Manak
- SeraCare Life Sciences, Inc., Gaithersburg, Maryland
| | - Silvana Sina
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Indira Hewlett
- U.S. Food and Drug Administration, CBER, Bethesda, Maryland
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Jerome Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Susan L. Stramer
- American Red Cross, Scientific Support Office, Gaithersburg, Maryland
| | - Ester Sabino
- Department of Infectious Disease/University of São Paulo, São Paulo, Brazil
| | - Piotr Grabarczyk
- Institute of Haematology and Blood Transfusion Medicine, Warsaw, Poland
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Sheila Peel
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Marco Schito
- Henry M. Jackson Foundation, Contractor to the Division of AIDS, NIH, Bethesda, Maryland
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14
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Vazquez F, Otero L, Melón S, de Oña M. Overview of molecular biological methods for the detection of pathogens causing sexually transmitted infections. Methods Mol Biol 2012; 903:1-20. [PMID: 22782808 DOI: 10.1007/978-1-61779-937-2_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We review here different state-of-the-art molecular methods currently used in the diagnosis of sexually transmitted infections.
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Affiliation(s)
- Fernando Vazquez
- Servicio de Microbiología, Hospital Monte Naranco, Oviedo, Spain.
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15
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Chudy M, Weber-Schehl M, Pichl L, Jork C, Kress J, Heiden M, Funk MB, Nübling CM. Blood screening nucleic acid amplification tests for human immunodeficiency virus Type 1 may require two different amplification targets. Transfusion 2011; 52:431-9. [PMID: 21810100 DOI: 10.1111/j.1537-2995.2011.03281.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Five cases of human immunodeficiency virus Type 1 (HIV-1) RNA-positive blood donations are described that escaped detection by three different CE-marked nucleic acid amplification technique (NAT) screening assays. These events were associated with two HIV-1 transmissions to recipients of blood components. The implicated NAT assays are monotarget assays and amplify in different viral genome regions (group-specific antigen or long terminal repeat). Investigations into the cause of the false-negative test results were initiated. STUDY DESIGN AND METHODS Plasma specimens of the five NAT false-negative cases were comparatively investigated in 12 CE-marked HIV-1 NAT systems of differing design. The relative amplification efficiency for the HIV-1 variant was determined for each assay. Sequencing of the variants in the region targeted by each false-negative NAT assay allowed comparison with the respective primers and probes. RESULTS Some of the NAT assays designed in a similar way to false-negative monotarget NATs also revealed deficiencies in detecting the viral variants. In each case sequencing of the assay target region in the variants demonstrated mismatches with primers and probes used by the assays. Some dual-target assays showed decreased amplification efficiency, but not false-negative results. CONCLUSION HIV is characterized by its rapid evolution of new viral variants. The evolution of new sequences is unpredictable; NAT screening assays with a single target region appear to be more vulnerable to sequence variations than dual-target assays. Based on this experience with false-negative tests results by monotarget NAT assays, the Paul-Ehrlich-Institut is considering requesting dual-target NAT assays for HIV-1 blood donation screening in Germany.
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16
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Amendola A, Bloisi M, Marsella P, Sabatini R, Bibbò A, Angeletti C, Capobianchi MR. Standardization and performance evaluation of "modified" and "ultrasensitive" versions of the Abbott RealTime HIV-1 assay, adapted to quantify minimal residual viremia. J Clin Virol 2011; 52:17-22. [PMID: 21764631 DOI: 10.1016/j.jcv.2011.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 04/08/2011] [Accepted: 04/25/2011] [Indexed: 11/28/2022]
Abstract
BACKGROUND Numerous studies investigating clinical significance of HIV-1 minimal residual viremia (MRV) suggest potential utility of assays more sensitive than those routinely used to monitor viral suppression. However currently available methods, based on different technologies, show great variation in detection limit and input plasma volume, and generally suffer from lack of standardization. OBJECTIVES In order to establish new tools suitable for routine quantification of minimal residual viremia in patients under virological suppression, some modifications were introduced into standard procedure of the Abbott RealTime HIV-1 assay leading to a "modified" and an "ultrasensitive" protocols. STUDY DESIGN The following modifications were introduced: calibration curve extended towards low HIV-1 RNA concentration; 4 fold increased sample volume by concentrating starting material; reduced volume of internal control; adoption of "open-mode" software for quantification. Analytical performances were evaluated using the HIV-1 RNA Working Reagent 1 for NAT assays (NIBSC). Both tests were applied to clinical samples from virologically suppressed patients. RESULTS The "modified" and the "ultrasensitive" configurations of the assay reached a limit of detection of 18.8 (95% CI: 11.1-51.0 cp/mL) and 4.8 cp/mL (95% CI: 2.6-9.1 cp/mL), respectively, with high precision and accuracy. In clinical samples from virologically suppressed patients, "modified" and "ultrasensitive" protocols allowed to detect and quantify HIV RNA in 12.7% and 46.6%, respectively, of samples resulted "not-detectable", and in 70.0% and 69.5%, respectively, of samples "detected <40 cp/mL" in the standard assay. CONCLUSIONS The "modified" and "ultrasensitive" assays are precise and accurate, and easily adoptable in routine diagnostic laboratories for measuring MRV.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of Virology, INMI L. Spallanzani, Via Portuense 292, 00149 Rome, Italy.
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