Journal of Clinical Virology最新文献

{"title":"Evaluation of Cepheid Xpert Xpress CoV-2/Flu/RSV plus for nasal and nasopharyngeal specimens tested in CLIA-accredited and CLIA-waived settings","authors":"Erin McElvania ,&nbsp;Deepa Rao ,&nbsp;Alexander L. Greninger ,&nbsp;Glenn Harnett ,&nbsp;Allan Larcena ,&nbsp;Amrish Patel ,&nbsp;Brian Webster ,&nbsp;Christina Ulen ,&nbsp;Dallas F. Green ,&nbsp;Dana King ,&nbsp;Deepesh Rubin Patel ,&nbsp;Imad Jandali ,&nbsp;Jane Gibson ,&nbsp;Jennifer Killion ,&nbsp;Jibran Atwi ,&nbsp;Kelly R. Bergmann ,&nbsp;Lance Slade ,&nbsp;Mary Allen Staat ,&nbsp;Matthew Faron ,&nbsp;Megan Washington ,&nbsp;Xiaohong Liu","doi":"10.1016/j.jcv.2025.105851","DOIUrl":"10.1016/j.jcv.2025.105851","url":null,"abstract":"<div><h3>Background</h3><div>Respiratory viruses are responsible for millions of healthcare visits annually. The unpredictable periodicity of Coronavirus disease 2019 and seasonal patterns of influenza and respiratory syncytial virus result in concurrent circulation of these viruses with non-specific and overlapping clinical symptoms.</div></div><div><h3>Study design</h3><div>This study evaluated the Cepheid Xpert Xpress CoV-2/Flu/RSV plus test using 3011 nasopharyngeal swab (NPS) and 2943 anterior nasal (NS) specimens. The assay was evaluated in CLIA-accredited (CA) laboratories with laboratory trained operators and CLIA-waived (CW) settings with non-laboratory personnel. Results were compared to the BioFire Respiratory Panel 2.1 for SARS-CoV-2 and Hologic Panther Fusion Flu A/B/RSV for influenza A, influenza B, and RSV. Cepheid Xpert Xpress CoV-2/Flu/RSV plus testing of NPS and NS specimens had high positive and negative agreement with reference testing.</div></div><div><h3>Results</h3><div>Overall agreement for NPS was 98.8 %, 99.1 %, 99.9 %, and 100 % for SARS-CoV-2, influenza A, influenza B, and RSV, respectively. For NS, overall agreement was 98.7 %, 99.3 %, 99.9 %, and 99.9 % for SARS-CoV-2, influenza A, influenza B, and RSV, respectively. Specimen testing performed at CA and CW locations also had high positive and negative agreement with reference testing. Overall agreement for CA testing was 97.7 %, 99.6 %, 100 %, and 100 % for SARS-CoV-2, influenza A, influenza B, and RSV, respectively. For CW testing, overall agreement was 98.8 %, 99.0 %, 99.9 %, and 99.9 % for SARS-CoV-2, influenza A, influenza B, and RSV, respectively.</div></div><div><h3>Conclusions</h3><div>This study demonstrates that Xpert Xpress CoV-2/Flu/RSV plus provides rapid and accurate results from NPS and NS specimens in CA and CW testing facilities regardless of staff experience with molecular testing.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105851"},"PeriodicalIF":3.4,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144840769","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":"Phylodynamics of human metapneumovirus and evidence for a duplication-deletion model in G gene variant evolution","authors":"Stephanie Goya ,&nbsp;Ethan B. Nunley ,&nbsp;Preston C. Longley ,&nbsp;Jamie R. Mathis ,&nbsp;Christina G. Varela ,&nbsp;Da Yae Kim ,&nbsp;Marc Nurik ,&nbsp;Samia N. Naccache ,&nbsp;Alexander L. Greninger","doi":"10.1016/j.jcv.2025.105848","DOIUrl":"10.1016/j.jcv.2025.105848","url":null,"abstract":"<div><h3>Background</h3><div>In December 2024, human metapneumovirus (hMPV) gained global attention amid rising cases in Chinese hospitals, prompting a World Health, Organization (WHO) statement indicating case numbers remained within expected ranges. To assess whether a variant of public health concern was emerging and to examine global hMPV phylodynamics, we conducted a genomic surveillance study in western Washington State.</div></div><div><h3>Study design</h3><div>We sequenced hMPV genomes from inpatient and outpatient samples collected between 2021 and 2025 in western Washington State and constructed phylogenomic and phylodynamic trees.</div></div><div><h3>Results</h3><div>We obtained 60 hMPV-A and 39 hMPV-B genomes, including 13 from November 2024 to January 2025. Following COVID-19 pandemic disruptions, hMPV seasonality returned to typical patterns after 2023. Genomic analysis showed hMPV-A predominance since 2022–23, with co-circulation of A2b1, A2b2, B1, and B2 sublineages. The A2b2 sublineage was most prevalent and all genomes carried a 111-nt G gene duplication. Phylogenetic evidence suggests the 111-nt variant evolved from a prior 180-nt duplication via a 69-nt deletion rather than through independent duplication events. Most sublineages showed multiple co-circulating clades, except A2b1. Phylodynamics showed recovery of global diversity after pandemic-related declines and a higher evolutionary rate in hMPV-A compared to hMPV-B. No distinct evolutionary features of heightened concern were detected.</div></div><div><h3>Conclusions</h3><div>Despite recent concerns, our findings indicate that hMPV circulation in, the USA follows expected seasonal patterns, with ongoing introductions of diverse viral variants from preexisting sublineages rather than emergence of a novel variant. Continued genomic surveillance is essential, particularly as vaccine development progresses.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105848"},"PeriodicalIF":3.4,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779933","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":"Gestational age-dependent dynamics of transplacental CMV and VZV IgG transfer: Weekly comparative analysis in preterm and full-term neonates (24–41 weeks)","authors":"Niko Kohmer ,&nbsp;Clara Seitz-Lüdeke ,&nbsp;Thorsten Mosler ,&nbsp;Alfred Lennart Bissinger ,&nbsp;Ulrich Rochwalsky ,&nbsp;Holger F. Rabenau ,&nbsp;Horst Buxmann","doi":"10.1016/j.jcv.2025.105847","DOIUrl":"10.1016/j.jcv.2025.105847","url":null,"abstract":"<div><h3>Background</h3><div>Transplacental transfer of maternal IgG antibodies promotes foetal immunity against cytomegalovirus (CMV) and varicella-zoster virus (VZV) infections. Comprehensive data on antibody transfer across gestational ages, particularly before 28 weeks, remain limited.</div></div><div><h3>Methods</h3><div>This prospective cohort study analysed paired maternal and newborn blood samples from n = 564 mother–child pairs (gestational weeks 24–41). Anti-CMV and anti-VZV IgG concentrations were measured using ELISA-tests and CMV neutralising capacity was assessed using an in-house cell culture-based assay.</div></div><div><h3>Results</h3><div>Newborn antibody concentrations were significantly lower than maternal levels at 24–29 weeks for both CMV and VZV (p &lt; 0.05). Equilibrium was reached at weeks 30–34 for CMV and 30–33 for VZV. Beyond week 35 for CMV and week 34 for VZV, newborn concentrations significantly surpassed maternal levels (p &lt; 0.05). CMV neutralisation capacity in neonates was significantly lower during weeks 24–29 compared to weeks 30–34 (p &lt; 0.05) and weeks 35–41 (p &lt; 0.01), showing progressive improvement during gestation. Maternal neutralising capacity remained constant across all gestational intervals. The newborn-maternal difference in neutralising capacity was progressive: minimal at weeks 24–29, significantly greater at weeks 30–34 (p &lt; 0.05), and maximum levels in neonates at weeks 35–41 (p &lt; 0.01), indicating enhanced qualitative antibody transfer. Neither gender nor twin-pregnancies showed a significant effect on antibody transfer.</div></div><div><h3>Conclusions</h3><div>Gestational age-dependent transplacental CMV and VZV IgG antibody transfer occurs as early as week 24. Extremely preterm infants showed significantly lower antibody concentrations and CMV neutralising capacity. Targeted prevention strategies for this vulnerable population and further studies investigating the preferential materno-foetal transfer of antibodies with high neutralisation capacities are warranted.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105847"},"PeriodicalIF":3.4,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144831033","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":"Clinical performance of the BD Onclarity™ HPV extended genotyping assay for anal cancer screening: a prospective pilot study","authors":"Anna Daniela Iacobone ,&nbsp;Fabio Bottari ,&nbsp;Davide Radice ,&nbsp;Silvia Martella ,&nbsp;Pietro Soru ,&nbsp;Cristian Mauro ,&nbsp;Chiara Scacchi ,&nbsp;Clementina Di Tonno ,&nbsp;Rita Passerini ,&nbsp;Cristina Trovato","doi":"10.1016/j.jcv.2025.105846","DOIUrl":"10.1016/j.jcv.2025.105846","url":null,"abstract":"<div><h3>Objectives</h3><div>To evaluate the clinical performance of an extended HPV genotyping assay for anal cancer screening in high-risk populations and investigate the prevalence of high-risk HPV (HR-HPV) genotypes in patients diagnosed with anal intraepithelial neoplasia grade 2 or worse (AIN2+).</div></div><div><h3>Study design</h3><div>A prospective cohort study was conducted at the European Institute of Oncology, Milan, Italy, from September 2022 to September 2024. A total of 202 high-risk individuals were enrolled. Anal samples were collected using a brush in ThinPrep PreservCyt from all subjects for HPV testing and genotyping; cytology was performed unless histology was already available. Associations between variables and sex were tested. Sensitivity, specificity, and predictive values for AIN2+ relative to HPV status were calculated. HR-HPV genotype prevalence was analysed in the overall population and among AIN2+ cases.</div></div><div><h3>Results</h3><div>The final study population comprised 192 subjects due to 10 invalid samples. No significant associations were found between patient characteristics and sex. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 87.7 % (95 % CI: 76.3–94.9), 72.6 % (95 % CI: 64.3–79.9), 57.5 % (95 % CI: 46.4–68.0), and 93.3 % (95 % CI: 86.7–97.3), respectively. Approximately 30 % of subjects were diagnosed with AIN2+. HR-HPV genotype distribution was similar between women and men. HPV16 was predominant in AIN2+ cases (&gt;70 %), followed by the 33/58 and 56/59/66 pools in women.</div></div><div><h3>Conclusions</h3><div>Extended HPV genotyping may support anal cancer screening strategies by providing a potential standalone tool for both screening and triage. Further studies are needed to confirm these findings in larger cohorts.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105846"},"PeriodicalIF":3.4,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144771306","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":"SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing","authors":"Keith Farrugia ,&nbsp;Zain Khalil ,&nbsp;Adriana van de Guchte ,&nbsp;Bremy Alburquerque ,&nbsp;Daniel Floda ,&nbsp;PSP Study Group ,&nbsp;Komal Srivastava ,&nbsp;Luz H. Patiño ,&nbsp;Juan David Ramirez ,&nbsp;Alberto E. Paniz-Mondolfi ,&nbsp;Emilia Mia Sordillo ,&nbsp;Viviana Simon ,&nbsp;Ana S. Gonzalez-Reiche ,&nbsp;Harm van Bakel","doi":"10.1016/j.jcv.2025.105845","DOIUrl":"10.1016/j.jcv.2025.105845","url":null,"abstract":"<div><h3>Background</h3><div>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) are characterized by distinct mutations in the S1 domain of the viral spike protein. This domain encompasses the N-terminal domain, the receptor-binding domain, and part of the cleavage site region. While mutations in other genomic regions of SARS-CoV-2 can impact VOC potential, the S1 domain holds particular importance for identifying variants and assessing antigenic evolution and immune escape potential.</div></div><div><h3>Methods</h3><div>We describe a rapid high-throughput sequencing-based assay, SpikeID, for the unbiased detection and identification of SARS-CoV-2 variants based on spike S1 amplicon sequencing. We benchmarked the SpikeID assay against Illumina whole-genome sequencing across 622 clinical biospecimens, representing lineages that circulated globally from October 2021 to January 2024.</div></div><div><h3>Results</h3><div>SpikeID unambiguously detected 100 % of WHO-designated VOCs and identified PANGO lineages circulating at ≥1 % prevalence in the New York City (NYC) area with 93 % accuracy in comparison to whole-genome sequencing. This reduction in accuracy was largely due to PANGO lineages that are only distinguishable by mutations outside the S1 domain.</div></div><div><h3>Conclusions</h3><div>We demonstrate the utility and scalability of the SpikeID assay during the emergence and subsequent surge of Omicron and Omicron-derived lineages in New York City, and show that our approach enables cost-effective, reliable, and near-real-time detection of emerging lineages.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105845"},"PeriodicalIF":3.4,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144779932","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":"Clinical evaluation of Xpert HIV Qual XC assay in diverse HIV-1 subtypes circulating in China","authors":"Jiafeng Zhang ,&nbsp;Xiaobei Ding ,&nbsp;Qin Fan ,&nbsp;Xinghui Gao ,&nbsp;Mingli Zhu ,&nbsp;Wenjie Luo ,&nbsp;Yan Xia ,&nbsp;Yiwei Tang ,&nbsp;Chengliang Chai ,&nbsp;Jianmin Jiang","doi":"10.1016/j.jcv.2025.105844","DOIUrl":"10.1016/j.jcv.2025.105844","url":null,"abstract":"<div><h3>Background</h3><div>Early and accurate HIV-1 diagnosis is crucial for timely treatment initiation and transmission prevention. This study evaluated the clinical performance of the Xpert HIV Qual XC assay in detecting HIV-1 across diverse subtypes in China.</div></div><div><h3>Methods</h3><div>A total of 242 whole blood samples (215 HIV-1-positive, 15 negative, plus 12 with non-HIV pathogens) were tested. Sensitivity, specificity, kappa coefficient, and correlations between Ct values and log₁₀ viral loads were analyzed. Operational performance was compared to the COBAS AmpliPrep/COBAS TaqMan HIV-1 Qualitative Test v2.0 (referred to as the COBAS system) regarding turnaround time (TAT) and reagent usage efficiency.</div></div><div><h3>Results</h3><div>The Xpert assay demonstrated a high sensitivity of 99.07 % and a specificity of 100.00 %, with an overall agreement of 99.18 % with clinical diagnoses. The detection rates varied by viral load and achieved 100.00 % accuracy for samples with viral loads above 50 copies/mL, but decreased to 84.62 %(11/13) for samples with extremely low viral loads (&lt;50 copies/mL). The assay successfully detected a wide range of HIV-1 subtypes, including CRF07_BC, CRF01_AE, and CRF08_BC, which reflects the genetic diversity in China. Additionally, the Xpert assay provides rapid results within 90 min and requires fewer reagents than COBAS system, making it a viable point-of-care testing option.</div></div><div><h3>Conclusions</h3><div>The Xpert HIV Qual XC assay shows excellent performance across diverse HIV-1 subtypes and is well-suited for decentralized diagnostic settings, supporting improved early diagnosis of HIV and treatment efforts.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105844"},"PeriodicalIF":3.4,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768717","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":"Emergence of Parechovirus-A5 central nervous system infections in children from Kansas City, Missouri, USA","authors":"Debarpan Dhar ,&nbsp;Anjana Sasidharan ,&nbsp;Katelyn E. VanDonge ,&nbsp;Brian Lee ,&nbsp;Maria Deza-Leon ,&nbsp;Christopher J. Harrison ,&nbsp;Dithi Banerjee ,&nbsp;Rangaraj Selvarangan","doi":"10.1016/j.jcv.2025.105835","DOIUrl":"10.1016/j.jcv.2025.105835","url":null,"abstract":"<div><h3>Background</h3><div>Parechovirus-A5 (PeV-A5) blood and central nervous system (CNS) infections are rare in the United States of America (USA) and globally. We report an emergence of PeV-A5 infections among infants in Kansas City, Missouri, in 2024.</div></div><div><h3>Methods</h3><div>Cerebrospinal fluid (CSF) and blood samples from infants were tested for Parechovirus-A (PeV-A) in 2024 as a part of standard of care at Children's Mercy Kansas City (CM-KC). PeV-A testing included a two-step reverse transcriptase-polymerase chain reaction, and genotyping was conducted using Sanger sequencing. We analyzed the amino acid sequences and phylogeny of the 2024 PeV-A viruses and described the clinical characteristics of PeV-A infected infants.</div></div><div><h3>Results</h3><div>Among 211 CSF and 46 blood samples from 248 patients, 10 (4 %) PeV-A infected patients were detected (8 CSF, 2 blood). Genotyping was successful for viruses from 9 PeV-A infected patients, with 8 identified as PeV-A5 (6 CSF, 2 blood) and 1 as PeV-A4 (CSF). PeV-A5 viral sequences from CM-KC clustered with other known PeV-A5 sequences, being most similar (&gt;97 %) to a PeV-A5 viral sequence from Sapporo City, Japan, in 2018. PeV-A5 detections from CM-KC occurred with a summer-fall seasonality. All 8 PeV-A5 infected patients had symptoms of rash with less irritability and lower maximum temperature when compared to previous PeV-A3 and PeV-A4 infected patients at CM-KC.</div></div><div><h3>Conclusions</h3><div>PeV-A5 emerged as the predominant PeV-A genotype detected from sterile sites (CSF, blood) in infants in Kansas City, Missouri in 2024, representing the highest number of PeV-A5 systemic illness in infants in the USA within a year.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105835"},"PeriodicalIF":4.0,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144703721","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":"The Human Papillomavirus (HPV) Laboratory e-Manual: A comprehensive guide for HPV testing and research","authors":"Laila Sara Arroyo Mühr ,&nbsp;Carina Eklund ,&nbsp;Camilla Lagheden ,&nbsp;Rita Mariel Correa ,&nbsp;María Dolores Fellner ,&nbsp;Maria Alejandra Picconi ,&nbsp;Nazlı Songur ,&nbsp;Murat Gultekin ,&nbsp;Kate Cuschieri ,&nbsp;Jean-Luc Prétet ,&nbsp;Quentin Lepiller ,&nbsp;Alice Baraquin ,&nbsp;Steffi Silling ,&nbsp;Kristiane Søreng ,&nbsp;Milan Stosic ,&nbsp;Gro Kummeneje Presthus ,&nbsp;Marc Arbyn ,&nbsp;Michael Peeters ,&nbsp;Steven Van Gucht ,&nbsp;Elizaveta Padalko ,&nbsp;Joakim Dillner","doi":"10.1016/j.jcv.2025.105834","DOIUrl":"10.1016/j.jcv.2025.105834","url":null,"abstract":"<div><h3>Background</h3><div>Human Papillomavirus (HPV) vaccination and HPV-based cervical cancer screening are central pillars of the World Health Organization (WHO) global cervical cancer elimination strategy. The WHO HPV Laboratory Manual, published in 2009, has provided essential guidance to promote an internationally comparable quality of HPV testing for many years. As the development in this area is rapid, the Global Network of National HPV Reference Laboratories considered that there is a need for an updated HPV Laboratory e-Manual to serve as a comprehensive and interactive resource for professionals engaged in quality-assured HPV testing for research and/or HPV-based cancer control.</div></div><div><h3>Content</h3><div>The HPV Laboratory e-Manual covers key areas, including laboratory quality assurance, HPV taxonomy and risk association, collection and handling of specimens, nucleic acid extraction, HPV detection and typing, HPV serology, data management, and the use of international standards. It provides up-to-date protocols and best practices to enhance accuracy and reliability of HPV testing. Interactive features allow for real-time updates, making it a dynamic resource for laboratories worldwide. The e-Manual is freely available at: https://www.hpvcenter.se/hpv-laboratory-manual/.</div></div><div><h3>Collaborators</h3><div>The e-Manual has been developed by international experts from 11 countries, including contributors from the International HPV Reference Center (IHRC, Sweden), the CDC’s Global HPV Reference Laboratory (USA), and multiple National HPV Reference Laboratories (NRLs). The standard procedure for writing a chapter was that 2 NRLs authored the chapter and 1 other NRL reviewed it.</div></div><div><h3>Conclusion</h3><div>The HPV Laboratory e-Manual represents a step toward global harmonization in laboratory methodologies for HPV testing, underpinning both research and cervical cancer control efforts.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"179 ","pages":"Article 105834"},"PeriodicalIF":4.0,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144605541","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":"Differential severity of SARS-CoV-2 variant infections in children and adults with COVID-19","authors":"Noah Brazer ,&nbsp;Venice Servellita ,&nbsp;Chengshi Jin ,&nbsp;Abiodun Foresythe ,&nbsp;Miriam Oseguera ,&nbsp;Jenny Nguyen ,&nbsp;Nanami Sumimoto ,&nbsp;Hee Jae Huh ,&nbsp;Andries Feder ,&nbsp;Sanchita Bhattacharya ,&nbsp;Surabhi Bhaskar ,&nbsp;Alicia Sotomayor-Gonzalez ,&nbsp;Prachi Saldhi ,&nbsp;Chris Choi ,&nbsp;Grace X. Li ,&nbsp;Komal Gopchandani ,&nbsp;Ashley Tippett ,&nbsp;Hui-Mien Hsiao ,&nbsp;Mark D. Gonzalez ,&nbsp;Dalia Gulick ,&nbsp;Charles Y. Chiu","doi":"10.1016/j.jcv.2025.105833","DOIUrl":"10.1016/j.jcv.2025.105833","url":null,"abstract":"<div><div>We performed virus whole-genome sequencing of 6916 upper respiratory swabs from adults and children from March 2020 to May 2023 and collected clinical metadata to assess differences in SARS-CoV-2 variant severity and symptomatology. Multivariable logistic regression showed a severity peak with Delta, which had the highest likelihood of severe infection. In children, another peak was observed with BA.4/BA.5, which was associated with more severe infection than both prior (BA.1) and later (BQ.1, BF.7, and XBB) Omicron variants. In contrast, BA.4/BA.5 in adults was associated with less severe infection than BA.1. Genome-wide association studies revealed that nonstructural protein 5 (nsp5, also called 3C-chymotrypsin-like protease), the Paxlovid target, and the spike N-terminal domain were strongly associated with severity. Kmers (contiguous nucleotide sequences of a fixed length k) from these regions matched the prototype Wuhan sequence exactly, corroborating decreases in severity over time. One kmer in the spike gene region was conserved in Delta genomes, with the kmer retained in higher proportions in patients with more severe infection. Our results show, with the exception of Delta, decreases in severity associated with SARS-CoV-2 variant infection over time and underscore the potential utility of kmer monitoring to assess variant severity.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105833"},"PeriodicalIF":4.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144634511","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":"Evaluation of molecular detection for respiratory syncytial viruses in World Health Organization Europe region laboratories, 2020–2023","authors":"Lance D. Presser ,&nbsp;Amani Yousef ,&nbsp;Elaine McCulloch ,&nbsp;Julia Schaumburg ,&nbsp;Adam Meijer","doi":"10.1016/j.jcv.2025.105832","DOIUrl":"10.1016/j.jcv.2025.105832","url":null,"abstract":"<div><h3>Background</h3><div>Respiratory syncytial virus (RSV) is a common pathogen causing mostly mild-symptoms, but in young infants and elderly individuals it can lead to severe disease and death. After the SARS-CoV-2 pandemic, more focus on and testing of patients with respiratory symptoms occurred, which led to an increase in RSV detections. Also, newly developed vaccines and prophylactic and therapeutic antibodies against RSV have been approved for use, increasing attention on the need for quality RSV diagnostics.</div></div><div><h3>Objectives</h3><div>The goal of this study was a broad analysis of the external quality assessment (EQA) data for RSV using data from Quality Control for Molecular Diagnostics (QCMD).</div></div><div><h3>Results</h3><div>Using the QCMD data, performance of NAATs for detecting RSV was evaluated on an average of 67 laboratories per year, in an average of 21 countries across the WHO Europe region. The results of these EQAs show that the performance of laboratories for RSV molecular diagnostics in the WHO Europe region is good; overall correct scores for core samples between 96.8 % and 99.2 % for RSV-A and between 96.0 % and 100 % for RSV-B for the years 2020–2023. For the years 2020–2023, more tests were performed using commercial assays (63.5–82.0 %) than in-house assays (18.0–36.5 %).</div></div><div><h3>Conclusions</h3><div>Based on analysis of data from the QCMD RSV EQA program during the years 2020–2023, we conclude molecular diagnostics for RSV in laboratories from WHO Europe region are being performed with high-quality. However, with increases in testing, numerous diagnostic assays being used by laboratories, and possible viral changes to newly introduced vaccines and prophylactic/therapeutic antibodies, continued quality assessment of RSV diagnostics is recommended.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"179 ","pages":"Article 105832"},"PeriodicalIF":4.0,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144597093","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}