Journal of Clinical Virology最新文献

{"title":"Feasibility, performances and predictive value of congenital CMV neonatal screening on saliva swabs","authors":"Vincent Portet Sulla ,&nbsp;Barkwendé Kabore ,&nbsp;Rana Rafek ,&nbsp;Amal Chaghouri ,&nbsp;Gwenaëlle Decombe ,&nbsp;Julia Lubrano Di Ciccone ,&nbsp;Lina Mouna ,&nbsp;Emmanuelle Letamendia-Richard ,&nbsp;Christelle Vauloup-Fellous","doi":"10.1016/j.jcv.2024.105713","DOIUrl":"10.1016/j.jcv.2024.105713","url":null,"abstract":"<div><h3>Background</h3><p>Early diagnosis of congenital CMV infection (cCMVI) allows for early intervention and follow-up to detect delayed hearing loss. While CMV PCR in urine is the gold standard for cCMVI diagnosis, saliva testing is often performed.</p></div><div><h3>Objectives</h3><p>Our aim was to determine (i) if swab saliva sampling needed standardization, (ii) if a threshold value in “virus copies per million cells (Mc)” in saliva samples could improve clinical specificity, and (iii) to establish a correlation between viral load in saliva and symptomatology/outcome of cCMVI.</p></div><div><h3>Materials and methods</h3><p>In our institution, universal newborn screening is performed on saliva swabs at delivery or until day 3 of life. If positive, CMV PCR in urine is done within 2 weeks to confirm or exclude cCMVI.</p></div><div><h3>Results</h3><p>Cell quantification showed that saliva swab sampling was well performed as 95.4 % samples had more than 100 cells/10 µL. There was a good correlation between saliva viral load in copies/mL and in copies/Mc (Pearson's <em>r</em> = 0.96, <em>p</em> &lt; 0.0001). However, threshold values, established to determine a viral load level at which we could confidently identify infected newborns, did not improve positive predictive value (21.8 % for copies/mL and 21 % for copies/Mc vs 25.4 % without threshold) but instead reduced sensitivity (88 % and 85% vs 100 % without threshold). Samples collected on day 2 or 3 had better positive predictive value (38.7 %) compared to those collected on day 1 (23.8 %). Symptomatology at birth was not significantly associated with viral load in saliva at diagnosis. However, sequelae occurrence was associated with viral load in saliva (copies/Mc).</p></div><div><h3>Discussion</h3><p>Our results confirm that saliva swab is a suitable sample for universal neonatal screening. However, identifying newborns that will develop sequelae remains an issue in the management of cCMVI.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105713"},"PeriodicalIF":4.0,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141709597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance evaluation of the new Access HIV Ag/Ab combo assay on the DxI 9000 Access Immunoassay Analyzer","authors":"V. Lemée ,&nbsp;S. Gréaume ,&nbsp;J. Gautier ,&nbsp;S.A. Dzamitika ,&nbsp;C. Coignard ,&nbsp;S.A. Jortani ,&nbsp;B. Grillet ,&nbsp;M. Badawi ,&nbsp;J-C. Plantier","doi":"10.1016/j.jcv.2024.105712","DOIUrl":"10.1016/j.jcv.2024.105712","url":null,"abstract":"<div><p>Fourth-generation HIV immunoassays have been developed to reduce the window period of detection during seroconversion period, allowing for the detection of early and established infections. The aim of this work was to evaluate a newly developed assay, Access HIV Ag/Ab combo on the novel high throughput DxI 9000 Access Immunoassay Analyzer (Beckman Coulter, Inc.). The assay allows for simultaneous qualitative detection and differentiation of HIV-1 p24 antigen and HIV-1/2 antibodies.</p><p>Assay performance was compared to two gold standard assays, the Abbott Architect HIV Ag/Ab Combo and Roche Elecsys HIV Duo, and assessed in a multicenter study, using a wide panel of samples (<em>n</em> &gt; 9000, clinical samples and viral lysates) representative of genetic diversity for both antibodies and antigens, early phases of infection, negative, and cross-reacting samples.</p><p>The clinical sensitivity was 100 % for clinical samples as well as for viral lysates. Data on viral lysates and early detection on seroconversion panels showed a better result with the Access assay. Analytical sensitivity showed a limit of p24 detection determined around 0.2 IU/mL. The overall specificity was 99.91 %, and no interference was found using the potentially cross-reactive samples.</p><p>In conclusion, the Access HIV Ag/Ab combo assay demonstrated its ability for accurate diagnosis of chronic as well as primary HIV infections on the DxI 9000 Analyzer, despite the high level of genetic diversity of these viruses.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105712"},"PeriodicalIF":4.0,"publicationDate":"2024-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S138665322400074X/pdfft?md5=213d9b5ccd1f8f2991aaf89265074c9c&pid=1-s2.0-S138665322400074X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141715637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A systematic review and meta-analysis of the risk of hepatitis B virus (HBV) resistance in people treated with entecavir or tenofovir","authors":"Sheila F. Lumley ,&nbsp;Marion Delphin ,&nbsp;Jolynne F. Mokaya ,&nbsp;Cedric C.S. Tan ,&nbsp;Emily Martyn ,&nbsp;Motswedi Anderson ,&nbsp;Ka Chun Li ,&nbsp;Elizabeth Waddilove ,&nbsp;Gloria Sukali ,&nbsp;Louise O. Downs ,&nbsp;Khadija Said ,&nbsp;Dorcas Okanda ,&nbsp;Cori Campbell ,&nbsp;Eli Harriss ,&nbsp;Yusuke Shimakawa ,&nbsp;Philippa C. Matthews","doi":"10.1016/j.jcv.2024.105711","DOIUrl":"10.1016/j.jcv.2024.105711","url":null,"abstract":"<div><h3>Background</h3><p>As nucleos/tide analogue (NA) therapy (e.g. entecavir and tenofovir) for chronic Hepatitis B virus (HBV) infection becomes more widely indicated and available, understanding drug resistance is essential. A systematic review to quantify resistance to these agents has not previously been undertaken.</p></div><div><h3>Methods</h3><p>We performed a systematic review and random-effects meta-analysis to estimate the risk of HBV resistance to entecavir and tenofovir. We searched nine databases up to 29-Aug-23. We included studies of HBV infection featuring &gt;10 individuals, written in English, reporting treatment ≥48 weeks, with assessment of HBV resistance based on viral sequence data. Data were analysed according to prior exposure history to NA, and choice of NA agent. Analyses were performed in R.</p></div><div><h3>Findings</h3><p>62 studies involving a total of 12,358 participants were included. For entecavir, in treatment-naive individuals (22 studies; 4326 individuals), resistance increased over time to 0.9 % at ≥5 years (95 %CI 0.1–2.3 %), and resistance was increased in NA-experienced individuals (18 studies; 1112 individuals), to 20.1 % (95 %CI 1.6–50.1 %) at ≥5 years. For tenofovir, pooled resistance risk was 0.0 % at all time points, whether previously NA naive (11 studies; 3778 individuals) or experienced (19 studies; 2059 individuals). There was a lack of consistent definitions, poor global representation and insufficient metadata to support subgroup analysis.</p></div><div><h3>Interpretation</h3><p>We have generated the first pooled estimates of HBV entecavir and tenofovir resistance over time. HBV resistance to entecavir in treatment-experienced groups in particular may represent a clinical and public health challenge. To date, tenofovir appears to have an excellent resistance profile, but due to data gaps, we caution that existing studies under-estimate the true real-world risk of resistance. Robust prospective data collection is crucial to reduce health inequities and reduce blind-spots in surveillance as treatment is rolled out more widely<strong>.</strong></p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105711"},"PeriodicalIF":4.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000738/pdfft?md5=7361359e6e45827959a63a40bf06b041&pid=1-s2.0-S1386653224000738-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141590443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of dried blood spots for Epstein–Barr virus nucleic acid testing","authors":"Mei Peng ,&nbsp;Hui-Lan Li ,&nbsp;Aixia Zhai,&nbsp;Qian-Ying Zhu","doi":"10.1016/j.jcv.2024.105710","DOIUrl":"https://doi.org/10.1016/j.jcv.2024.105710","url":null,"abstract":"<div><p>Epstein–Barr virus (EBV) is a ubiquitous and oncogenic virus that is associated with various malignancies and non-malignant diseases and EBV DNA detection is widely used for the diagnosis and prognosis prediction for these diseases. The dried blood spots (DBS) sampling method holds great potential as an alternative to venous blood samples in geographically remote areas, for individuals with disabilities, or for newborn blood collection. Therefore, the objective of this study was to assess the viability of detecting EBV DNA load from DBS. Matched whole blood and DBS samples were collected for EBV DNA extraction and quantification detection. EBV DNA detection in DBS presented a specificity of 100 %. At different EBV DNA viral load in whole blood, the sensitivity of EBV DNA detection in DBS was 38.78 % (≥1 copies/mL), 43.18 % (≥500 copies/mL), 58.63 % (≥1000 copies/mL), 71.43 % (≥2000 copies/mL), 82.35 % (≥4000 copies/mL), and 92.86 % (≥5000 copies/mL), respectively. These results indicated that the sensitivity of EBV DNA detection in DBS increased with elevating viral load. Moreover, there was good correlation between EBV DNA levels measured in whole blood and DBS, and on average, the viral load measured in whole blood was about 6-fold higher than in DBS. Our research firstly demonstrated the feasibility of using DBS for qualitative and semi-quantitative detection of EBV DNA for diagnosis and surveillance of EBV-related diseases.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105710"},"PeriodicalIF":4.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141483212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Does the ultrasensitive HBsAg Next assay enhance Hepatitis B diagnosis? An evaluation of analytical performances","authors":"Joachim Bourdin ,&nbsp;Pierre Sellier ,&nbsp;Maud Salmona ,&nbsp;Caroline Lascoux-Combe ,&nbsp;Constance Delaugerre ,&nbsp;Sarah Maylin","doi":"10.1016/j.jcv.2024.105707","DOIUrl":"10.1016/j.jcv.2024.105707","url":null,"abstract":"<div><h3>Background</h3><p>Accurate laboratory confirmation for Hepatitis B diagnosis and monitoring are crucial. Recently an ultrasensitive immunoassay test, the HBsAg Next (HBsAgNx), has been reported approximately eight times more sensitive than current HBsAg assays. The aim of our study was to assess the analytical performances of this new test.</p></div><div><h3>Methodology</h3><p>253 clinical samples from Saint Louis University Hospital were analyzed, splitted into four panels: (<span>1</span>) routine prospectively screening serums (<em>n</em> = 196), (<span>2</span>) retrospective serum samples before HBV reactivation (HBV-R) (<em>n</em> = 18), (<span>3</span>) occult HBV infection (OBI) (<em>n</em> = 10) and (<span>4</span>) a selection of wild type HBV genotypes (<em>n</em> = 29)</p></div><div><h3>Results</h3><p>Panel 1, showed robust agreement with the HBsAg Qualitative II (HBsAgQII) assay (Cohen's kappa = 0.83). Despite this agreement, 7 false positive with the HBsAgQII assay were found negative with HBsAgNx. One OBI was detected only with HBsAgNx. Panel 2 showed potential time savings in diagnosing HBV-R using HBsAgNx among 4/18 HBsAg positives samples. Panel 3 highlighted the ability of HBsAgNx to detect HBsAg in OBI patients defined by negative for HBsAg with HBsAgQII assay and positive for HBV DNA. Furthermore, the HBsAgNx assay detected all different genotypes.</p></div><div><h3>Conclusion</h3><p>The study highlights the effectiveness of the HBsAgNx assay, showing its performance. It excels in detecting weakly positive samples and addressing challenging cases. HBsAgNx assay demonstrates promising analytical performances, with improved sensitivity and specificity compared to standard HBsAgQII assay, able to detect all genotypes. Its potential impact on early detecting and monitoring reactivations, and occult infections could be very useful in clinical practice.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105707"},"PeriodicalIF":4.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141534561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of a rapid recency assay for detection of early HIV infection","authors":"Clara Di Germanio ,&nbsp;Xutao Deng ,&nbsp;Eduard Grebe ,&nbsp;Jeffrey A. Johnson ,&nbsp;Silvina Masciotra ,&nbsp;Michael P. Busch ,&nbsp;Philip J. Norris","doi":"10.1016/j.jcv.2024.105708","DOIUrl":"10.1016/j.jcv.2024.105708","url":null,"abstract":"<div><p>The Asanté HIV-1 Rapid Recency assay's ‘verification’ line detected HIV infection a median of 18 days later than a nucleic acid detection assay and performed similarly to 19 other existing rapid HIV antibody tests. Pending regulatory approval, the assay could be an option with other rapid tests in national HIV-1 testing algorithms, which would allow collection of HIV recency data as part of a national screening program without requiring additional testing.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105708"},"PeriodicalIF":4.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance","authors":"Rosa C. Coldbeck-Shackley ,&nbsp;Penelope J. Adamson ,&nbsp;Daryn Whybrow ,&nbsp;Caitlin A. Selway ,&nbsp;Lito E. Papanicolas ,&nbsp;Mark Turra ,&nbsp;Lex E.X. Leong","doi":"10.1016/j.jcv.2024.105709","DOIUrl":"10.1016/j.jcv.2024.105709","url":null,"abstract":"<div><h3>Background</h3><p>Human Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (<em>pol)</em> sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis.</p></div><div><h3>Methods</h3><p>We implemented dWGS and performed parallel <em>pol</em> Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis.</p></div><div><h3>Results</h3><p>Optimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of <em>pol</em> sequence alone.</p></div><div><h3>Conclusions</h3><p>These findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional <em>pol</em> sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105709"},"PeriodicalIF":4.0,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000714/pdfft?md5=7ed4ba8f5f74ab1a945c420c41a73fc3&pid=1-s2.0-S1386653224000714-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical performance of the Roche Cobas Liat SARS-CoV-2 & influenza A/B assay: A systematic review and meta-analysis","authors":"Eunjin Chang ,&nbsp;Kibum Jeon ,&nbsp;Nuri Lee ,&nbsp;Min-Jeong Park ,&nbsp;Wonkeun Song ,&nbsp;Hyun Soo Kim ,&nbsp;Han-Sung Kim ,&nbsp;Jae-Seok Kim ,&nbsp;Jimin Kim ,&nbsp;Seri Jeong","doi":"10.1016/j.jcv.2024.105706","DOIUrl":"10.1016/j.jcv.2024.105706","url":null,"abstract":"<div><p>Respiratory tract infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses are persistent and critical. The Cobas Liat SARS-CoV-2 &amp; influenza A/B assay (Multiplex Liat), the FDA-authorized point-of-care reverse transcriptase polymerase chain reaction (RT-PCR) assay, has a turnaround time of 20 min and high accuracy. This study evaluates the pooled performance of this assay to provide practical information. This meta-analysis was registered in PROSPERO (registration number: CRD42023467579). A systematic literature search was conducted within PubMed, Ovid-EMBASE, and the Cochrane Library for articles evaluating the accuracy of the Multiplex Liat assay through September 2023. A random-effects model was used to calculate the pooled diagnostic values with real-time RT-PCR (rRT-PCR) as a reference test. A total of 4,705 samples from eight studies were included in the primary meta-analysis. The overall pooled sensitivity and specificity of Multiplex Liat were 100.0 % (95 % confidence interval [CI] = 96.7 %–100.0 %) and 99.7 % (95 % CI = 98.7 %–99.9 %), respectively. The presence of variants of concern or in-house rRT-PCR assays as reference standards did not significantly affect the pooled diagnostic performance of the Multiplex Liat. When 5,333 samples from nine studies were assessed for sensitivity, the pooled sensitivity was 100.0 % (95 % CI = 85.8 %–100.0 %) without a significant difference. This meta-analysis demonstrates the usefulness of Multiplex Liat for the detection of SARS-CoV-2 based on pooled diagnostic values. These practical findings may facilitate appropriate settings for the diagnosis and management of patients with respiratory tract infections.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"174 ","pages":"Article 105706"},"PeriodicalIF":4.0,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000684/pdfft?md5=3155d214245d6a8c7954b3981595fcb1&pid=1-s2.0-S1386653224000684-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141389457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Melting curve analysis reveals false-positive norovirus detection in a molecular syndromic panel","authors":"Nancy Matic ,&nbsp;Tanya Lawson ,&nbsp;Matthew Young ,&nbsp;Willson Jang ,&nbsp;Jennifer Bilawka ,&nbsp;Leah Gowland ,&nbsp;Gordon Ritchie ,&nbsp;Victor Leung ,&nbsp;Michael Payne ,&nbsp;Aleksandra Stefanovic ,&nbsp;Marc G. Romney ,&nbsp;Christopher F. Lowe","doi":"10.1016/j.jcv.2024.105697","DOIUrl":"10.1016/j.jcv.2024.105697","url":null,"abstract":"<div><h3>Background</h3><p>Molecular syndromic panels can improve rapidity of results and ease clinical laboratory workflow, although caution has been raised for potential false-positive results. Upon implementation of a new panel for infectious diarrhea (BioFire® FilmArray® Gastrointestinal [GI] Panel, bioMérieux) in our clinical laboratory, a higher than expected number of stool samples with norovirus were detected.</p></div><div><h3>Objectives</h3><p>The goal of this study was to investigate positive percent agreement and the false-positive rate of norovirus detected by the multiplex BioFire GI panel compared to a singleplex commercial assay.</p></div><div><h3>Study design</h3><p>From October 2023 to January 2024, all prospective stool samples with a positive norovirus result by BioFire had melting curves reviewed manually using the BioFire FilmArray Torch System. Stool samples further underwent testing by a supplementary real-time RT-PCR assay (Xpert® Norovirus, Cepheid) for comparative analysis.</p></div><div><h3>Results</h3><p>Of the 50 stool samples with norovirus detected by BioFire, 18 (36 %) tested negative by Xpert (deemed \"false-positives\"). Furthermore, melting curve analysis revealed nearly all of these samples had atypical melting curve morphologies for the \"Noro-1\" target on BioFire (16/18, 89 %), which was statistically significant (Odds Ratio 173.2, 95 % CI [22.2, 5326.9], <em>p</em> &lt; 0.0001). Stool samples with multiple pathogens detected by BioFire including norovirus were not more likely to produce false-positive norovirus results (Odds Ratio 1, 95 % CI [0.3, 3.3], <em>p</em> = 1).</p></div><div><h3>Conclusions</h3><p>Although not described in the manufacturer's <em>Instructions for Use</em>, we propose routine manual review of melting curves for the BioFire GI panel prior to reporting, to mitigate potential false-positive norovirus results.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"173 ","pages":"Article 105697"},"PeriodicalIF":8.8,"publicationDate":"2024-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1386653224000593/pdfft?md5=c423b5c837627ec86baa64edd7c77889&pid=1-s2.0-S1386653224000593-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141183853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics","authors":"F. Xavier Lopez-Labrador ,&nbsp;Michael Huber ,&nbsp;Igor A. Sidorov ,&nbsp;Julianne R. Brown ,&nbsp;Lize Cuypers ,&nbsp;Lies Laenen ,&nbsp;Bert Vanmechelen ,&nbsp;Piet Maes ,&nbsp;Nicole Fischer ,&nbsp;Ian Pichler ,&nbsp;Nathaniel Storey ,&nbsp;Laura Atkinson ,&nbsp;Stefan Schmutz ,&nbsp;Verena Kufner ,&nbsp;Sander van Boheemen ,&nbsp;Claudia E. Mulders ,&nbsp;Adam Grundhoff ,&nbsp;Patrick Blümke ,&nbsp;Alexis Robitaille ,&nbsp;Ondrej Cinek ,&nbsp;Jutte J.C. de Vries","doi":"10.1016/j.jcv.2024.105695","DOIUrl":"10.1016/j.jcv.2024.105695","url":null,"abstract":"<div><p>Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS).</p><p>A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline.</p><p>Overall, viral pathogens with loads down to 10⁴ copies/ml (corresponding to C_T values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of C_T values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively.</p><p>A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.</p></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"173 ","pages":"Article 105695"},"PeriodicalIF":8.8,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S138665322400057X/pdfft?md5=22ce2b90dc93fb6b9779951463075d74&pid=1-s2.0-S138665322400057X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141186679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}