Jean Luc Prétet, Laila Sara Arroyo Mühr, Kate Cuschieri, María Dolores Fellner, Rita Mariel Correa, María Alejandra Picconi, Suzanne M Garland, Gerald L Murray, Monica Molano, Michael Peeters, Steven Van Gucht, Charlotte Lambrecht, Davy Vanden Broeck, Elizaveta Padalko, Marc Arbyn, Quentin Lepiller, Alice Brunier, Steffi Silling, Kristiane Søreng, Irene Kraus Christiansen, Mario Poljak, Camilla Lagheden, Emel Yilmaz, Carina Eklund, Hem R Thapa, Troy D Querec, Elizabeth R Unger, Joakim Dillner
BACKGROUND: Some high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL)...
February 20, 2024: Journal of Clinical Virology
Matthias E Futschik, Samuel Johnson, Elena Turek, David Chapman, Simon Carr, Zareen Thorlu-Bangura, Paul E Klapper, Malur Sudhanva, Andrew Dodgson, Joanna R Cole-Hamilton, Nick Germanacos, Raghavendran Kulasegaran-Shylini, Edward Blandford, Sarah Tunkel, Timothy Peto, Susan Hopkins, Tom Fowler
BACKGROUND: The advent of lateral flow devices (LFDs) for SARS-CoV-2 detection enabled widespread use of rapid self-tests during the pandemic. While self-testing using LFDs is now common, whether self-testing provides comparable performance to professional testing was a key question that remained important for pandemic planning. METHODS: Three prospective multi-centre studies were conducted to compare the performance of self- and professional testing using LFDs...
February 15, 2024: Journal of Clinical Virology
Pedro Pisa, Constance Wose Kinge, Charles Chasela, Eula Mothibi, Yin Min Thaung, Hnin T Thwin, Nay M Aung, Kara W Chew, Malini M Gandhi, Cavenaugh Clint, Thomas Minior, Aye A Lwin, Morgan J Freiman, Khin P Kyi, Yi Y Sein, Fadzai Marange, Charles van der Horst, Sofiane Mohamed, Matthieu Barralon, Ian Sanne
BACKGROUND: Developing countries experience limited access to HCV laboratory tests for different reasons. Providing near to real-time HCV testing and results especially to at-risk populations including those in rural settings for timely initiation to treatment is key. Within a rural Myanmar setting, we compared HCV diagnostic detection and quantification of the GeneXpert, and Advanced Biological Laboratories UltraGene-HCV assays against the gold standard and reference method Roche real-time HCV in Myanmar...
February 12, 2024: Journal of Clinical Virology
Mikayla Quinton, Duane W Newton, Becky Neil, Sondra Mitchell, Heba H Mostafa
INTRODUCTION: Quality control (QC) is one component of an overarching quality management system (QMS) that aims at assuring laboratory quality and patient safety. QC data must be acceptable prior to reporting patients' results. Traditionally, QC statistics, records, and corrective actions were tracked at the Johns Hopkins Molecular Virology Laboratory using Microsoft Excel. Unity Real-Time (UnityRT), a QMS software (Bio-Rad Laboratories), which captures and analyzes QC data by instrument and control lot per assay, was implemented and its impact on the workflow was evaluated...
February 12, 2024: Journal of Clinical Virology
Raquel Fernández-Moreno, Aurora Páez-Vega, Diego Rodríguez-Cano, Ana Salinas, Fernando Rodríguez-Cantalejo, Aurora Jurado, Julián Torre-Cisneros, Sara Cantisán
BACKGROUND: The QuantiFERONCMV (QF-CMV) assay is an interferon-gamma release assay (IGRA) used to monitor CMV-specific cell-mediated immunity (CMV-CMI) by ELISA in transplant patients. However, a chemiluminescent immunoassay (CLIA) has been developed to quantify IFNG in the QuantiFERON-Tuberculosis (TB) to detect latent TB infection. OBJECTIVES: The aim of this work is to compare the results of QF-CMV by ELISA with those obtained by CLIA in an automated Liaison XL analyzer using the QuantiFERON-TB Gold Plus reagents...
February 8, 2024: Journal of Clinical Virology
Assilina Parfut, Simona Tripon, Pierre Gantner, Fréderic Chaffraix, Elodie Laugel, Marie-Josée Wendling, Furkan Erol, Carine Wiedemer, Michel Doffoel, Antonio Saviano, Maude Royant, François Habersetzer, Samira Fafi-Kremer, Aurélie Velay
BACKGROUND: Hepatitis Delta virus (HDV) infection is a major cause of liver-related morbidity and mortality in patients infected with HBV, with a global HDV prevalence uncertain. In France, 2 to 5 % of HBs antigen (HBsAg) carriers present anti-HDV antibodies (anti-HDV). The EASL recommends testing for anti-HDV in all HBsAg-positive patients. Since January 2022, we have systematically carried out anti-HDV serology when a positive HBsAg is discovered (new HBsAg carriers). OBJECTIVES: We evaluated the benefit of anti-HDV reflex testing after one year of practice by comparing anti-HDV and HBsAg serology data over the last six years, among the new HBsAg carriers and all the HBsAg carriers...
February 3, 2024: Journal of Clinical Virology
D A M Heideman, J Berkhof, L Verhoef, C Ouwerkerk, P W Smit, A Oštrbenk Valenčak, J Mlakar, M Poljak, R D M Steenbergen, M C G Bleeker
BACKGROUND: Human papillomavirus (HPV) testing on self-samples is a valid tool for cervical cancer screening. HPV self-sample workflows need to be clinically validated to ensure safe use in screening. OBJECTIVE: This study evaluated the fully automated NeuMoDx HPV Assay self-sample workflow that is compiled of the NeuMoDx HPV assay and the NeuMoDx 96/288 Molecular Systems, for clinical performance and reproducibility on Evalyn Brush-collected self-samples. METHODS: The clinical performance of the NeuMoDx HPV Assay self-sample workflow for cervical intraepithelial neoplasia grade 2 or worse (CIN2+) and CIN3+ was evaluated on 987 self-samples obtained from women attending national organized HPV-based cervical cancer screening by a noninferiority analysis relative to reference workflows using either HPV-Risk Assay or high-risk HPV GP5+/6+-PCR...
February 1, 2024: Journal of Clinical Virology
Or Kriger, Sarah Dovrat, Ilana S Fratty, Eyal Leshem, Michal Tepperberg Oikawa, Danit Sofer, Sharon Amit
BACKGROUND: Varicella zoster virus (VZV) is among the leading pathogens causing meningitis and encephalitis. While VZV-PCR-positive CSF is considered a gold-standard for diagnosis, it is not-uncommon to detect VZV-DNA in CSF of patients with other acute or chronic illness. Our goal was to determine the clinical relevance of VZV-PCR-positive CSF when investigating patients with neurological symptoms. METHODS: In this retrospective cohort from the largest hospital in Israel, we collected demographic, clinical and laboratory data of patients with VZV-PCR-positive CSF, analyzing the significance of various parameters...
January 22, 2024: Journal of Clinical Virology
Emma Ann Davies, Laura Dutton, Malcolm Guiver
BACKGROUND: Human Adenoviruses are a common cause of disease and can cause significant morbidity and mortality in immunocompromised patients. Nosocomial transmission events can occur with whole genome sequencing playing a crucial role. This study evaluates the performance of a custom designed SureSelectXT target enrichment assay based on 14 adenovirus genomes for sequencing direct from clinical samples. METHODS: Modifications were made to the SureSelectXT low input protocol to enhance performance for viral targets...
January 11, 2024: Journal of Clinical Virology
Sung Yong Park, Gina Faraci, Kevin Ganesh, Michael P Dubé, Ha Youn Lee
BACKGROUND: Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care. METHODS: We developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals)...
January 9, 2024: Journal of Clinical Virology
M Schneider, K Kollender, B Hilfrich, R Weiss, T Iftner, A Heim, T Ganzenmueller
BACKGROUND: Reliable and fast detection and quantification of human cytomegalovirus (CMV) DNA in various diagnostic specimens is essential for care of immunocompromised or congenitally infected individuals. OBJECTIVES: To evaluate the analytical and clinical performance of the Panther Aptima® CMV (Hologic) quantitative real-time transcription mediated amplification (TMA) assay. STUDY DESIGN: Performance of the TMA assay run on the Hologic Panther Fusion was analysed for 32 proficiency testing samples and 21 quantitative reproducibility panel samples; additionally, we compared results of TMA assay and routine quantitative real-time PCR assays ("PCR-A"= Biomérieux CMV R-gene® or "PCR-B"= Laboratory-developed CMV-PCR) in 518 diagnostic specimens (254 plasma, 120 EDTA whole blood, 43 urine, 45 amniotic fluid and 56 breast milk) at two university hospital laboratories...
January 1, 2024: Journal of Clinical Virology
Anja Oštrbenk Valenčak, Kate Cuschieri, Linzi Connor, Andrej Zore, Špela Smrkolj, Mario Poljak
Human papillomavirus (HPV)-based screening offers better protection against cervical cancer compared to cytology, but HPV screening assays must adhere to validation requirements of the international guidelines to ensure optimal performance. Allplex HPV HR Detection (Allplex) assay, launched in the late 2022, is a fully automated real-time PCR-based assay utilizing innovative technology that enables quantification and concurrent distinction of 14 high-risk HPV genotypes (HPV16,18,31,33,35,39,45,51,52,56,58,59,66 and 68)...
January 1, 2024: Journal of Clinical Virology
Paul Loubet, Jérôme Fernandes, Gérard de Pouvourville, Katia Sosnowiez, Anne Elong, Caroline Guilmet, Hanane Omichessan, Isabelle Bureau, Francis Fagnani, Corinne Emery, Claire Nour Abou Chakra
BACKGROUND: Respiratory syncytial virus (RSV) causes lower respiratory tract infections (LRTI) that may lead to hospitalization or death. The present study aimed to assess the burden of RSV infections in hospitalized adults. METHODS: RSV-related hospitalizations were identified from the nationwide hospital claims database in France (PMSI) from 2012 to 2021 using ICD-10 codes J12.1, J20.5, J21.0 or B97.4, and outcomes assessment focused on 2016-2020. In-hospital outcomes included length of stay, need for intensive care (ICU) and in-hospital all-cause mortality...
December 31, 2023: Journal of Clinical Virology
Ameeka Thompson, David Hettle, Stephanie Hutchings, Barry Vipond, Nicholas Veasey, Kerry Grant, Jonathan Turner, Rich Hopes, Jonathan Steer, Rommel Ravanan, O Martin Williams, Peter Muir
BACKGROUND: Prompt identification of patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection on admission to hospital is crucial to ensuring initiation of appropriate treatment, optimising infection control and maintaining patient flow. The Abbott ID NOW™ COVID-19 assay (ID NOW) is a point-of-care, isothermal nucleic acid amplification test, capable of producing a result within minutes, potentially placing it as an invaluable tool in helping to control the coronavirus-disease 2019 (COVID-19) pandemic...
December 13, 2023: Journal of Clinical Virology
Jonathan Reed, Ginger Kwak, Eli A Piliper, Emily J Degli-Angeli, Erin A Goecker, Alexander L Greninger
BACKGROUND: Cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA (usRNA) are important virological parameters for monitoring HIV-1 persistence and activation of latent HIV-1. Assays fully validated by CLIA and/or GCLP standards are needed for future clinical trials that seek to evaluate treatments directed towards HIV-1 cure. OBJECTIVES: To determine performance characteristics of sensitive, moderate-throughput, digital droplet PCR (ddPCR) assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 usRNA that can detect a broad range of HIV-1 M-group subtypes...
December 7, 2023: Journal of Clinical Virology
Marwa Khedhiri, Melek Chaouch, Kaouther Ayouni, Anissa Chouikha, Mariem Gdoura, Henda Touzi, Nahed Hogga, Alia Benkahla, Wasfi Fares, Henda Triki
West Nile Virus (WNV) causes a serious public health concern in many countries around the world. Virus detection in pathological samples is a key component of WNV infection diagnostic, classically performed by real-time PCR. In outbreak situation, rapid detection of the virus, in peripheral laboratories or at point of care, is crucial to guide decision makers and for the establishment of adequate action plans to prevent virus dissemination. Here, we evaluate a Loop-mediated isothermal amplification (LAMP) tool for WNV detection...
December 7, 2023: Journal of Clinical Virology
Samuel M S Cheng, Jonathan J Lau, Leo C H Tsang, Kathy Leung, Cheuk Kwong Lee, Asmaa Hachim, Niloufar Kavian, Sara Chaothai, Ricky W K Wong, Jennifer K M Yu, Zacary Y H Chai, Masashi Mori, Chao Wu, Karen Yiu, David S C Hui, Gaya K Amarasinghe, Leo L M Poon, Joseph T Wu, Sophie A Valkenburg, Malik Peiris
BACKGROUND: Natural SARS-CoV-2 infection may elicit antibodies to a range of viral proteins including non-structural protein ORF8. RNA, adenovirus vectored and sub-unit vaccines expressing SARS-CoV-2 spike would be only expected to elicit S-antibodies and antibodies to distinct domains of nucleocapsid (N) protein may reliably differentiate infection from vaccine-elicited antibody. However, inactivated whole virus vaccines may potentially elicit antibody to wider range of viral proteins, including N protein...
December 1, 2023: Journal of Clinical Virology
Erley Lizarazo Forero, Marjolein Knoester, Lilli Gard, Alewijn Ott, Afke H Brandenburg, Matthew B B McCall, Hubert G M Niesters, Coretta Van Leer-Buter
INTRODUCTION: Public health measures aimed at controlling transmission of SARS-CoV-2, otherwise known as "lockdown" measures, had profound effects on circulation of non-SARS viruses, many of which decreased to very low levels.  The interrupted transmission of these viruses may have lasting effects. Some of the influenza clades seem to have disappeared during this period, a phenomenon which is described as a "funnel effect". It is currently unknown if the lockdown measures had any effect on the diversity of circulating viruses, other than influenza...
December 2023: Journal of Clinical Virology
Raquel Giacomelli Cao, Asuncion Mejias, Amy L Leber, Huanyu Wang
BACKGROUND: Enterovirus-D68 (EV-D68) has appeared biennially in the United States following the 2014 outbreak. It has gained epidemiologic and clinical relevance and was identified as an important pathogen associated with severe respiratory and central nervous system diseases. We aim to describe the clinical and molecular characteristics of the post-pandemic 2022 Enterovirus-D68 outbreak in children evaluated in a tertiary pediatric hospital in Columbus, Ohio. METHODS: EV-D68 RT-PCR was performed on nasopharyngeal specimens collected during Jun-Nov 2022 from children (<18 years), identified by 1) physician-order or 2) random selection of 10-15 specimens weekly that were Rhinovirus/Enterovirus-positive by physician-ordered respiratory virus panel...
December 2023: Journal of Clinical Virology
Quentin Pangot, François Labaste, Vincent Pey, Chloé Médrano, Adam Tuijnman, Stéphanie Ruiz, Jean-Marie Conil, Vincent Minville, Fanny Vardon-Bounes
RATIONALE: Several authors have compared COVID-19 infection with influenza in the ICU. OBJECTIVE: This study aimed to compare the baseline clinical profiles, care procedures, and mortality outcomes of patients admitted to the intensive care unit, categorized by infection status (Influenza vs. COVID-19). METHODS: Retrospective observational study. Data were extracted from the Toulouse University Hospital from March 2014 to March 2021. To compare survival curves, we plotted the survival at Day-90 using the Kaplan-Meier curve and conducted a log-rank test...
December 2023: Journal of Clinical Virology
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