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Fahnøe U, Madsen LW, Christensen PB, Sølund CS, Mollerup S, Pinholt M, Weis N, Øvrehus A, Bukh J. Effect of direct-acting antivirals on the titers of human pegivirus 1 during treatment of chronic hepatitis C patients. Microbiol Spectr 2024; 12:e0064124. [PMID: 39051781 PMCID: PMC11370240 DOI: 10.1128/spectrum.00641-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024] Open
Abstract
Coinfections with human pegivirus 1 (HPgV-1) are common in chronic hepatitis C virus (HCV) patients. However, little is known about whether HPgV-1 is affected by direct-acting antivirals during HCV treatment. Metagenomic analysis and reverse transcriptase-quantitative PCR (RT-qPCR) were performed on RNA from the plasma of 88 selected chronic HCV patients undergoing medical treatment. Twenty (23%) of these HCV patients had HPgV-1 coinfections and were followed by RT-qPCR during treatment and follow-up to investigate HPgV-1 RNA titers. Recovered sequences could be assembled to complete HPgV-1 genomes, and most formed a genotype 2 subclade. All HPgV-1 viral genomic regions were under negative purifying selection. Glecaprevir/pibrentasvir treatment in five patients did not consistently lower the genome titers of HPgV-1. In contrast, a one log10 drop of HPgV-1 titers at week 2 was observed in 10 patients during treatment with sofosbuvir-containing regimens, sustained to the end of treatment (EOT) and in two cases decreasing to below the detection limit of the assay. For the five patients treated with ledipasvir/sofosbuvir with the inclusion of pegylated interferon, titers decreased to below the detection limit at week 2 and remained undetectable to EOT. Subsequently, the HPgV-1 titer rebounded to pretreatment levels for all patients. In conclusion, we found that HCV treatment regimens that included the polymerase inhibitor sofosbuvir resulted in decreases in HPgV-1 titers, and the addition of pegylated interferon increased the effect on patients with coinfections. This points to the high specificity of protease and NS5A inhibitors toward HCV and the more broad-spectrum activity of sofosbuvir and especially pegylated interferon. IMPORTANCE Human pegivirus 1 coinfections are common in hepatitis C virus (HCV) patients, persisting for years. However, little is known about how pegivirus coinfections are affected by treatment with pangenotypic direct-acting antivirals (DAAs) against HCV. We identified human pegivirus by metagenomic analysis of chronic HCV patients undergoing protease, NS5A, and polymerase inhibitor treatment, in some patients with the addition of pegylated interferon, and followed viral kinetics of both viruses to investigate treatment effects. Only during HCV DAA treatment regimens that included the more broad-spectrum drug sofosbuvir could we detect a consistent decline in pegivirus titers that, however, rebounded to pretreatment levels after treatment cessation. The addition of pegylated interferon gave the highest effect with pegivirus titers decreasing to below the assay detection limit, but without clearance. These results reveal the limited effect of frontline HCV drugs on the closest related human virus, but sofosbuvir appeared to have the potential to be repurposed for other viral diseases.
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Affiliation(s)
- Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Institute for Regional Health Research, University of Southern Denmark, Research Unit for Internal Medicine Kolding Hospital, Kolding, Denmark
| | - Peer Brehm Christensen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Christina Søhoel Sølund
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
| | - Sarah Mollerup
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Hvidovre, Denmark
| | - Anne Øvrehus
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Manso T, de Salazar A, Rodríguez-Velasco M, García F, Aguilera A. Detection and quantification of HBV and HCV in plasma samples by means of different molecular assays: Comparative study. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2024; 42:13-16. [PMID: 36624027 DOI: 10.1016/j.eimce.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/26/2022] [Accepted: 07/02/2022] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Viral load is a very useful marker for monitoring patients infected with HBV and HCV. This work compares assays based on transcription-mediated amplification (TMA) and on real-time PCR (RT-PCR) to verify whether they can be interchangeable. MATERIAL AND METHODS A bicentric study, in which 147 plasma samples from patients infected with HBV and 229 with HCV were analyzed, was carried out. TMA-based assays (Aptima® HBV Quant and Aptima® HCV Quant Dx, employing Panther system (Hologic®)) and RT-PCR (COBAS® AmpliPrep/COBAS® TaqMan® and COBAS® 6800) were used and the degree of concordance between them was calculated. RESULTS Viral load was detected in both systems in 60 (40.82%) HBV samples (median log viral load: COBAS: 2.51IU/mL (IQR 2.20-3.17), Panther: 2.71IU/mL (IQR 2.21-3.22)) and in 39 (16.96%) HCV samples (median log viral load: COBAS: 3.93IU/mL (IQR 2.24-6.01), Panther: 3.80IU/mL (IQR 1.99-6.14)). The agreement between both systems was κ=0.943 for HBV and κ=0.925 for HCV. Comparison of viral load samples detected by both assays showed a hight correlation for HBV (R2=0.86) and for HCV (R2=0.97). CONCLUSIONS Both TMA and RT-PCR based assays may be interchangeable for the management of patients infected with HBV and HCV.
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Affiliation(s)
| | - Adolfo de Salazar
- Hospital Universitario Clinico San Cecilio, Instituto de Investigacion Ibs.Granada, Granada, Spain
| | | | - Federico García
- Hospital Universitario Clinico San Cecilio, Instituto de Investigacion Ibs.Granada, Granada, Spain
| | - Antonio Aguilera
- Complejo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Castruita JAS, Schneider UV, Mollerup S, Leineweber TD, Weis N, Bukh J, Pedersen MS, Westh H. SARS-CoV-2 spike mRNA vaccine sequences circulate in blood up to 28 days after COVID-19 vaccination. APMIS 2023; 131:128-132. [PMID: 36647776 PMCID: PMC10107710 DOI: 10.1111/apm.13294] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
In Denmark, vaccination against Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has been with the Pfizer-BioNTech (BTN162b2) or the Moderna (mRNA-1273) mRNA vaccines. Patients with chronic hepatitis C virus (HCV) infection followed in our clinic received mRNA vaccinations according to the Danish roll-out vaccination plan. To monitor HCV infection, RNA was extracted from patient plasma and RNA sequencing was performed on the Illumina platform. In 10 of 108 HCV patient samples, full-length or traces of SARS-CoV-2 spike mRNA vaccine sequences were found in blood up to 28 days after COVID-19 vaccination. Detection of mRNA vaccine sequences in blood after vaccination adds important knowledge regarding this technology and should lead to further research into the design of lipid-nanoparticles and the half-life of these and mRNA vaccines in humans.
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Affiliation(s)
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | - Sarah Mollerup
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | - Thomas Daell Leineweber
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Department of Infectious Diseases, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark.,Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schou Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Manso T, de Salazar A, Rodríguez-Velasco M, García F, Aguilera A. Detección y cuantificación de VHB y VHC en muestras de plasma mediante la utilización de diferentes ensayos moleculares: estudio comparativo. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Park Y, Roh J, Kim S. Performance Evaluation of the Aptima Assays in Comparison with the cobas 6800 Assays for the Detection of HIV-1, HBV, and HCV in Clinical Samples. Ann Lab Med 2022; 42:447-456. [PMID: 35177565 PMCID: PMC8859551 DOI: 10.3343/alm.2022.42.4.447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/06/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Background Accurate and consistent viral load (VL) quantitation of HIV type 1 (HIV-1), hepatitis B virus (HBV), and hepatitis C virus (HCV) is important for diagnosis and clinical monitoring. Assay results have to be concordant and compatible across laboratories. We evaluated the performance of three Aptima assays (Hologic, San Diego, CA, USA) and compared their VL values with corresponding cobas 6800 assay (Roche Diagnostics, Mannheim, Germany) results, using 840 clinical samples. Methods The correlation between VL results obtained using the two assays was evaluated in terms of analytical sensitivity, precision/reproducibility, linearity, and cross-reactivity. Agreement rates were determined using kappa statistics. The overall agreement of VL values was examined using Passing–Bablok regression analysis. Results All CVs were within 5%; the assays had good precision for detecting all three viruses. The linearity of quantitation assessed using three AccuSpan linearity panels (Seracare, Milford, MA, USA), was excellent for the Aptima assays. For HIV-1 and HCV, the results of both assays showed excellent agreement (κ=0.89 and 0.90, respectively) while for HBV, the results showed good agreement (κ=0.69). For analytical sensitivity, the VLs required for a 100% detection rate of HIV-1, HBV, and HCV were 20 copies/mL, 7.5 IU/mL, and 5.0 IU/mL, respectively. The results for HIV-1, HBV, and HCV obtained using both assays correlated strongly (R2=0.97, 0.93, and 0.95, respectively). Conclusions The cobas 6800 and Aptima assays, with fully automated and high-throughput molecular platforms for HIV-1, HBV, and HCV VL measurements, show good analytical performance and a strong correlation between results. The study results suggest that the assays can be used interchangeably for long-term monitoring of chronic infections.
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Affiliation(s)
- Younhee Park
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Juhye Roh
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Murayama A, Momose H, Yamada N, Matsubayashi K, Muramatsu M, Hamaguchi I, Kato T. Performance Evaluation of In Vitro Screening and Diagnostic Kits for Hepatitis C Virus Infection. Front Cell Infect Microbiol 2022; 11:793472. [PMID: 35186779 PMCID: PMC8851425 DOI: 10.3389/fcimb.2021.793472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/07/2021] [Indexed: 11/24/2022] Open
Abstract
Aim A reliable kit with high sensitivity and specificity is indispensable for diagnosing hepatitis C virus (HCV) infection. Detection kits for anti-HCV antibodies (anti-HCV) are used for screening, and quantification kits for HCV RNA and HCV antigen (Ag) are used for the definite diagnosis of HCV infection or the evaluation of the pathological condition of and therapeutic effects in patients with chronic hepatitis C. Several kits are currently available for these purposes and are provided for clinical use in Japan. In this study, we aimed to evaluate the performance of these kits. Methods We used International Standards for HCV RNA and HCV Ag and a regional reference panel to evaluate the performance of thirteen anti-HCV, five HCV RNA, and two HCV Ag kits. Results All specimens in the regional reference panel were diagnosed correctly by all anti-HCV kits, although the distributions of the quantified values varied, and the ratios of titer classification were not identical across kits. All HCV RNA kits quantified the International Standard with minimum deviation and diagnosed the specimens of the reference panel correctly. The quantified values of the International Standard by two HCV Ag kits were inconsistent. HCV Ag titers of some specimens were underestimated owing to the amino acid polymorphisms in comparison with HCV RNA titers. Conclusions The evaluation with International Standards and the regional reference panel was useful for assessing the quality of screening and diagnostic kits for HCV infection, and such quality control is essential for the clinical usage of these kits.
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Affiliation(s)
- Asako Murayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Haruka Momose
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Norie Yamada
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keiji Matsubayashi
- Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Isao Hamaguchi
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takanobu Kato
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Takanobu Kato,
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7
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Lefeuvre C, Pivert A, Tran CT, Lunel-Fabiani F, Ducancelle A, Le Guillou-Guillemette H. Practical approach to method verification in plasma and validation in cerebrospinal fluid under accreditation using a flexible scope in molecular virology: setting up the HIV, HBV and HCV Aptima™ Quant Dx assays. Clin Chem Lab Med 2021; 58:251-260. [PMID: 31539347 DOI: 10.1515/cclm-2019-0502] [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: 05/17/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022]
Abstract
Background Our laboratory obtained the ISO 15189 accreditation for the plasmatic HIV-1, HBV and HCV viral load (VL) using the m2000 RealTime™ system, which was recently changed for the platform Panther®. Here, we discuss a strategy for performing method validation/verification very quickly. Methods We performed the mandatory (repeatability, internal quality assessment [IQA], measurement uncertainty [MU]) and optional technical verifications for CE/IVD assays using the flexible scope range A. We also performed the mandatory assays for the validation of HIV-1 VL in the cerebrospinal fluid (CSF) using the flexible scope range B. The change was checked by following up on the turnaround time (TAT). Results The coefficient of variation (CV%) for repeatability and IQA complied with the limit of 0.25 log. The MU results ranged from 0.04 to 0.25 log copies or IU/mL. The comparisons of methods showed excellent correlations (R2 = 0.96 for the three parameters) but a delayed centrifugation on HCV VL showed variations of up to 2 log IU/mL. An excellent linearity for HIV-1 in the CSF was obtained from 1.5 to 5 log copies/mL with R2 = 0.99. The TAT increased (84%-98%) in routine usage. Conclusions The three Aptima assays are well suited for routine laboratory use and can be integrated within less than 2 weeks in accordance with flexible scope range A. Our data allows us to confidently perform HIV-1 VL in CSF following flexible scope range B. Finally, we provide an organizational guide for flexible scope management in molecular virology within a short time frame.
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Affiliation(s)
- Caroline Lefeuvre
- Virology Department, Angers University Hospital, HIFIH Laboratory EA 3859, LUNAM, Angers, France
| | - Adeline Pivert
- Virology Department, Angers University Hospital, HIFIH Laboratory EA 3859, LUNAM, Angers, France
| | - Cong T Tran
- Virology Department, Angers University Hospital, HIFIH Laboratory EA 3859, LUNAM, Angers, France
| | - Françoise Lunel-Fabiani
- Virology Department, Angers University Hospital, HIFIH Laboratory EA 3859, LUNAM, Angers, France
| | - Alexandra Ducancelle
- Virology Department, Angers University Hospital, HIFIH Laboratory EA 3859, LUNAM, Angers, France
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Genome Sequence of an Unknown Subtype of Hepatitis C Virus Genotype 6: Another Piece for the Taxonomic Puzzle. Microbiol Resour Announc 2019; 8:8/42/e01030-19. [PMID: 31624172 PMCID: PMC6797537 DOI: 10.1128/mra.01030-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The surveillance and correct subtyping of hepatitis C virus strains require available and up-to-date publicly available reference genomes. Here, we present the complete open reading frame sequence of a hepatitis C virus genotype 6 strain of an unknown subtype that was discovered during routine subtyping of patients in the clinic. The surveillance and correct subtyping of hepatitis C virus strains require available and up-to-date publicly available reference genomes. Here, we present the complete open reading frame sequence of a hepatitis C virus genotype 6 strain of an unknown subtype that was discovered during routine subtyping of patients in the clinic.
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9
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Evaluation of the Aptima HCV Quant Dx Assay Using Serum and Dried Blood Spots. J Clin Microbiol 2019; 57:JCM.00030-19. [PMID: 30760534 DOI: 10.1128/jcm.00030-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 02/06/2019] [Indexed: 01/19/2023] Open
Abstract
Hepatitis C virus (HCV) RNA quantitation is the primary method by which active HCV infections are identified and the response to direct-acting antiviral therapy is monitored. This study describes the evaluation of the Aptima HCV Quant Dx assay (Aptima HCV) performed on the Panther system. The clinical performance of Aptima HCV was compared to that of the Cobas AmpliPrep/Cobas TaqMan HCV test v2.0 (CAP/CTM). Overall agreement was 84.9% (186/219) with a kappa statistic of 0.755 (standard error, 0.037; 95% confidence interval [CI], 0.682 to 0.828). Passing-Bablok regression of log10 IU/ml values revealed a regression line of Y = 1.163 × X - 0.991 (95% CI of the slope, 1.103 to 1.221, and intercept, -1.341 to -0.642). The 95% lower limit of detection (LLOD) for Aptima HCV on dried blood spot (DBS) samples was calculated to be 2.43 log10 IU/ml (267 IU/ml; 95% CI, 2.31 to 2.73 log10 IU/ml [204 to 540 IU/ml]). A comparison of Aptima HCV testing on paired DBS and serum specimens collected from patients at the time of routine blood collection for CAP/CTM demonstrated an overall agreement of 90.1% (82/91) with a kappa statistic of 0.657 (standard error, 0.101; 95% CI, 0.458 to 0.855). In conclusion, Aptima HCV provides a suitable alternative for HCV RNA testing on serum and DBS samples.
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10
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Catlett B, Carrera A, Starr M, Applegate TL, Lowe P, Grebely J, Philip Cunningham H. Performance evaluation of the Hologic Aptima HCV Quant Dx assay for detection of HCV RNA from dried blood spots. J Clin Virol 2019; 112:40-44. [PMID: 30776575 DOI: 10.1016/j.jcv.2019.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/14/2019] [Accepted: 01/24/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND The availability of effective direct-acting antiviral therapy for hepatitis C virus (HCV) has led to a need for simplified diagnostic pathways. Barriers to treatment uptake, specifically in people who inject drugs and in remote and resource limited settings, may be overcome by utilizing novel collection methods, such as dried blood spots (DBS). However, there are currently no registered assays for HCV RNA testing from DBS samples. OBJECTIVES To evaluate the sensitivity and specificity of the Aptima HCV Dx Quant assay for HCV RNA detection in DBS samples STUDY DESIGN: 107 paired venepuncture and DBS samples from HCV antibody positive individuals were analyzed for HCV RNA on the Aptima HCV Dx Quant and Roche CAP/CTM (gold standard) HCV assays. RESULTS 78% (n=83) had detectable HCV RNA in plasma. Sensitivity of the Aptima assay for HCV RNA detection in DBS was 96.4% (95% CI 89.8-99.3%) and specificity was 95.8% (95% CI 78.8-99.9%). Sensitivity for HCV RNA detection in DBS using a quantitative threshold of ≥15 IU/mL in plasma was 95.1% (95% CI 88%-98.7%) and specificity was 96.0% (95% CI 79.7%-99.9%). The sensitivity of HCV RNA detection in DBS using a quantitative threshold of ≥1000 IU/mL (based on a clinically relevant threshold) was 100% (95% CI 95.3-100%) and specificity was 100% (95% CI 88.4-100%). CONCLUSIONS Our data indicates that the Aptima HCV Dx Quant can detect active HCV infection from a DBS sample with good sensitivity and specificity, particularly when using a threshold of ≥1000 IU/mL.
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Affiliation(s)
- Beth Catlett
- NSW State Reference Laboratory for HIV, St Vincent's Centre for Applied Medical Research, Darlinghurst, Sydney, Australia; The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia.
| | - Alex Carrera
- NSW State Reference Laboratory for HIV, St Vincent's Centre for Applied Medical Research, Darlinghurst, Sydney, Australia
| | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St Vincent's Centre for Applied Medical Research, Darlinghurst, Sydney, Australia
| | - Tanya L Applegate
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Peter Lowe
- Hologic Australia, Macquarie Park, New South Wales, Australia
| | - Jason Grebely
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - H Philip Cunningham
- NSW State Reference Laboratory for HIV, St Vincent's Centre for Applied Medical Research, Darlinghurst, Sydney, Australia
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Outcome and adverse events in patients with chronic hepatitis C treated with direct-acting antivirals: a clinical randomized study. Eur J Gastroenterol Hepatol 2018; 30:1177-1186. [PMID: 29994874 DOI: 10.1097/meg.0000000000001192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE New potent direct-acting antiviral (DAA) regimens against hepatitis C virus have been approved in recent years. However, information about the rate of adverse events (AEs) across different DAA regimens is limited. We aimed to evaluate differences in AEs and treatment efficacy in patients with chronic hepatitis C (CHC), genotype (GT) 1 or 3, randomized to two different treatment arms, correspondingly. PATIENTS AND METHODS We randomly assigned 96 patients in a 1 : 1 ratio, to treatment for 12 weeks with either paritaprevir/ombitasvir/ritonavir/dasabuvir/ribavirin (RBV) or ledipasvir/sofosbuvir (SOF)/RBV if infected with GT1 (72 patients) or to daclatasvir/SOF/RBV for 12 weeks or SOF/RBV for 24 weeks, if infected with GT3 (24 patients). Data on AEs were collected throughout the entire study period. RESULTS A total of 70 (97%) patients with CHC with GT1 and 20 (83%) patients with GT3 achieved cure. The GT3 treatment arm was prematurely terminated, owing to change in national treatment guidelines. Thus, only AEs for GT1 patients are described. AEs occurred in 70 (97%) GT1 patients, and most common AEs were anemia (n=56/78%), fatigue (n=53/74%), and headache (n=33/46%). No difference was observed in relation to treatment group (P=1.0), anemia (P=1.0), or liver cirrhosis (P=0.53). In seven (11%) patients, AEs assessed by the investigator to be possibly related to the DAA regimen were still present 12 weeks after treatment. CONCLUSIONS We found no difference in AEs possibly related to the DAA regimen in patients with CHC, but surprisingly, AEs possibly related to the DAA regimen persisted in a significant number of patients after treatment. This finding can be of importance for clinicians in relation to patient information concerning AEs possibly related to DAA treatment.
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Pedersen MS, Fahnøe U, Hansen TA, Pedersen AG, Jenssen H, Bukh J, Schønning K. A near full-length open reading frame next generation sequencing assay for genotyping and identification of resistance-associated variants in hepatitis C virus. J Clin Virol 2018; 105:49-56. [PMID: 29886373 DOI: 10.1016/j.jcv.2018.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/22/2018] [Accepted: 05/26/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND The current treatment options for hepatitis C virus (HCV), based on direct acting antivirals (DAA), are dependent on virus genotype and previous treatment experience. Treatment failures have been associated with detection of resistance-associated substitutions (RASs) in the DAA targets of HCV, the NS3, NS5A and NS5 B proteins. OBJECTIVE To develop a next generation sequencing based method that provides genotype and detection of HCV NS3, NS5A, and NS5 B RASs without prior knowledge of sample genotype. STUDY DESIGN In total, 101 residual plasma samples from patients with HCV covering 10 different viral subtypes across 4 genotypes with viral loads of 3.84-7.61 Log IU/mL were included. All samples were de-identified and consequently prior treatment status for patients was unknown. Almost full open reading frame amplicons (∼ 9 kb) were generated using RT-PCR with a single primer set. The resulting amplicons were sequenced with high throughput sequencing and analysed using an in-house developed script for detecting RASs. RESULTS The method successfully amplified and sequenced 94% (95/101) of samples with an average coverage of 14,035; four of six failed samples were genotype 4a. Samples analysed twice yielded reproducible nucleotide frequencies across all sites. RASs were detected in 21/95 (22%) samples at a 15% threshold. The method identified one patient infected with two genotype 2b variants, and the presence of subgenomic deletion variants in 8 (8.4%) of 95 successfully sequenced samples. CONCLUSIONS The presented method may provide identification of HCV genotype, RASs detection, and detect multiple HCV infection without prior knowledge of sample genotype.
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Affiliation(s)
- M S Pedersen
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Department of Science and Environment, Roskilde University, Denmark
| | - U Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - T A Hansen
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - A G Pedersen
- DTU Bioinformatics, Technical University of Denmark, Denmark
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Denmark
| | - J Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases and Clinical Research Centre, Copenhagen University Hospital, Hvidovre, And Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - K Schønning
- Department of Microbiology, Copenhagen University Hospital, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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