Journal of Clinical Virology最新文献

{"title":"The impact of blood pressure indicators and shock indices on hazard of complicated dengue in hospitalized adults with dengue infection","authors":"Baihui Xu ,&nbsp;Tun-Linn Thein ,&nbsp;Zong Min Tay ,&nbsp;Yee-Sin Leo ,&nbsp;David Chien Lye ,&nbsp;Po Ying Chia ,&nbsp;Jue Tao Lim","doi":"10.1016/j.jcv.2025.105855","DOIUrl":"10.1016/j.jcv.2025.105855","url":null,"abstract":"<div><div>Blood pressure monitoring is crucial for early detection of complicated dengue. We investigated the association between blood pressure indicators and complicated dengue hazard over the course of dengue hospitalization in a well-characterized dengue cohort. This study involved 4789 adult dengue patients hospitalized between 2005 and 2008 who did not have complicated dengue (defined as dengue haemorrhagic fever and/or severe dengue) initially. Cases (n = 689) included patients who progressed to complicated dengue during hospitalization, while controls were patients who did not (n = 4100). We used Cox models with time-dependent covariates to estimate hazard ratios for blood pressure indicators' impact on complicated dengue hazard. Additionally, we employed the overlap weighting approach to balance clinical characteristics and conducted subgroup analyses based on age, sex and warning signs. Results indicated that modified shock index (MSI) <span><math><mo>≥</mo></math></span>0.8 was associated with a higher time-averaged hazard in the main cohort (HR: 1.72 [1.36, 2.19], p-value: &lt;0.01). Shock index (SI) ≥0.7 also indicated increased hazard in the main cohort (HR: 1.64 [1.37, 1.95], p-value: &lt;0.01) and among patients without mucosal bleeding (HR: 1.42 [1.19, 1.72], p-value: &lt;0.01). A DBP &lt;60 mmHg led to higher hazards of complicated dengue (HR: 1.45 [1.23, 1.72], p-value: &lt;0.01) in the main cohort. In conclusion, DBP &lt;60 mmHg, shock index <span><math><mo>≥</mo></math></span>0.7 and modified shock index <span><math><mo>≥</mo></math></span>0.8 may be reliable predictors for complicated dengue during hospitalization in adult dengue patients. Clinicians should consider these indices during patient assessment.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105855"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911951","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":"2025-10-01","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":"Impact on hospital length of stay and antimicrobial usage in children diagnosed with viral meningitis by rapid multiplexed PCR assay","authors":"Jacky Lu ,&nbsp;Jessica Flores-Vazquez ,&nbsp;Jaehyeon Lee ,&nbsp;Leila C. Posch ,&nbsp;Cristina Costales ,&nbsp;Jennifer Dien Bard","doi":"10.1016/j.jcv.2025.105856","DOIUrl":"10.1016/j.jcv.2025.105856","url":null,"abstract":"<div><div>Meningitis and encephalitis can lead to severe morbidity and result in permanent neurologic deficits in children, but outcomes differ depending on the causative pathogen. Early diagnosis of viral meningitis may allow for appropriate management, including avoidance of antimicrobial treatment and hospital admission. We sought to determine the clinical utility of a multiplexed meningitis-encephalitis (ME) panel at a quaternary care pediatric institution in patients diagnosed with human enterovirus (HEV) and human parechovirus (HPeV) meningitis. Retrospective analysis of patients between June 2016 and October 2023 positive for HEV or HPeV (n = 66) by ME panel were compared to HEV or HPeV positive patients (n = 53) diagnosed by standalone PCR (polymerase chain reaction) between December 2011 and May 2016. The turnaround time (TAT) for ME panel was 2.67 h compared to 22.05 h for standalone polymerase chain reaction (PCR) (p &lt; 0.0001). In patients with cerebrospinal fluid (CSF) collected and tested by ME panel within 72 h of admission compared to standalone PCR, the duration of intravenous acyclovir therapy was significantly reduced (3.88 vs 16.03 h, P = 0.03). Despite viral detection by molecular methods, patients remained on antibiotics until CSF cultures were confirmed to be negative after 48 h of incubation. Implementation of ME panel in a pediatric hospital improved overall time to diagnosis of viral (or aseptic) ME. Although not statistically significant, the median length of stay (LOS) of patients positive for HEV or HPeV by ME panel was reduced by 0.51 days when compared to standalone PCR (1.95 vs. 2.46 days, p = 0.66).</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"Article 105856"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144885699","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":"Pathogen surveillance of acute conjunctivitis reveals recent emergence of coxsackievirus A24 variants and high genotypic diversity of human adenoviruses in Shenzhen, China, 2018-2024.","authors":"Long Chen, Hong Yang, Hai-Long Zhang, Xiao-Lu Shi, Bo Peng, Jun Meng","doi":"10.1016/j.jcv.2025.105852","DOIUrl":"10.1016/j.jcv.2025.105852","url":null,"abstract":"<p><strong>Objectives: </strong>To investigate the etiological characteristics of acute conjunctivitis in Shenzhen, China.</p><p><strong>Methods: </strong>A total of 1234 conjunctival swabs collected between 2018 and 2024 were examined for coxsackievirus A24 variant (CVA24v), enterovirus D70 (EV-D70) and human adenovirus (HAdV). Complete VP1 sequences of CVA24v strains were determined and analyzed. HAdV was genotyped by PCR methods targeting the three genes (penton base, hexon and fiber) and sequencing. SPSS 22.0 software was used for statistical analysis.</p><p><strong>Results: </strong>CVA24v was first detected in 2023, with a detection rate of 33.3 % (63/189). No EV-D70 was detected in 2018-2024. The annual distributions of HAdV-infected patients were 52.6 % (101/192), 62.7 % (111/177), 21.1 % (37/175), 9.0 % (14/155), 10.5 % (17/162), 15.9 % (30/189) and 21.7 % (40/184), respectively. CVA24v strains from this study clustered in a clade with significant temporal aggregation characteristic within the genotype GIV. Eight amino acid variation sites (T11A, I16L, K20I, L32P, K105R, A146T, R277G and P280S) were observed in VP1 sequences of CVA24v strains from this study when compared to the close strains. Conjunctivitis patients with one of the three symptoms (weakness, fever and blurred vision) had a higher detection rate of HAdV. Eleven known HAdV genotypes (HAdV-B3, -B14, -B21, HAdV-D8, -D37, -D42, -D53, -D64, -D85, -D115 and HAdV-E4) and 7 unknown genotypes were detected in 2020-2024, with HAdV-D37 (30.9 %), HAdV-D115 (21.1 %) and HAdV-B3 (17.1 %) being the three predominant genotypes.</p><p><strong>Conclusions: </strong>The unique genetic characteristics were observed in Shenzhen CVA24v strains. HAdVs associated with conjunctivitis exhibited a high degree of genotypic diversity in Shenzhen, and HAdV-D115 related to conjunctivitis was first reported in this study.</p>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"105852"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812096","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":"Heterogeneity of false reactivity profiles of HIV assays while optimizing national HIV testing algorithms: Findings from a multi-country analysis.","authors":"Manfred Accrombessi, Cheryl Johnson, Alaleh Abadpour, Jean De Dieu Anoubissi, Joseph Fokam, Araz Chiloyan, Iryna Andrianova, Hamakwa Mantina, Agai Kherbino Akec, Fatou Ousmane Sall, Abdelaye Keita, Elizabeth Telan, Adoum Fouda Abderrazzack, Chatté Adawaye, Rose Wafula, Stephen Ayisi-Addo, Monkoe S Leqheka, Jacob Lusekelo Mwambeta, Jeremie Muwonga Masidi, Dramane Kania, Anita Sands, Rachel Baggaley, Jean-François Etard, Céline Lastrucci","doi":"10.1016/j.jcv.2025.105843","DOIUrl":"10.1016/j.jcv.2025.105843","url":null,"abstract":"<p><p>This study highlights the importance of verifying HIV testing algorithms to reduce the risk of misdiagnoses caused by common false reactivity. Between 2020 and 2023, WHO supported 14 countries to assess rates of false reactivity and shared false reactivity across HIV rapid diagnostic tests (RDTs) used in HIV testing services. The study involved 26,278 results from 22 different RDT products, with sample sizes ranging from 100 to 302 results per country. The number of RDT products assessed varied between 4 and 13 per country. False reactivity rates ranged from 0 % to 3.32 %, with one country reporting a high false reactivity rate of over 4 % for one RDT. Five countries have no shared false reactivity between RDTs, while the remaining eight countries shared false reactivity across one to six pairs of RDT products. These findings were used to inform national policy, with more than 90 % of countries introducing new RDT products into their HIV testing algorithm based on these results. The study concludes that rates of false reactivity and shared false reactivity between RDT products vary across countries. Therefore, conducting verification studies is crucial for updating national HIV testing algorithms and ensuring accurate diagnosis while also facilitating the market entry of new HIV testing products.</p>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"105843"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12439682/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816831","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":"Performance of a commercial assay for detecting JC Polyomavirus DNA in human samples.","authors":"Sébastien Lhomme, Isabelle Da Silva, Oriane Cabanel, Estelle Raguin, Guillaume Martin-Blondel, Nassim Kamar, Jacques Izopet, Florence Abravanel","doi":"10.1016/j.jcv.2025.105849","DOIUrl":"10.1016/j.jcv.2025.105849","url":null,"abstract":"<p><strong>Introduction: </strong>We evaluated the performance of the automated AltoStar JCV PCR platform for detecting and quantifying JC Polyomavirus (JCPyV) DNA in samples including urine, plasma and cerebrospinal fluid.</p><p><strong>Methods and results: </strong>Using the NIBSC JCPyV DNA standard, the assay was linear from 1 to 6 log IU/mL standard and the limit of detection determined by Probit analysis corresponded to 9.3 [95 % CI: 7.0-16.5] IU/mL. Specificity was accessed by testing urines containing a high concentration of BK Polyomavirus; none tested positive for JCPyV. The intra-run and inter-run standard deviations were 0.02 IU/mL and 0.35 IU/mL, respectively. Lastly, clinical performance was determined by testing 45 samples quantified previously with a laboratory-developed test (LDT). The assays were concordant for 42/45 samples. One of the 3 samples that tested negative with the AltoStar assay had a low JCpyV DNA concentration. We were unable to re-test the 3 negative samples due to insufficient volume. A conservation problem could not be ruled out for the 3 samples with discordant results.</p><p><strong>Conclusions: </strong>The AltoStar platform enables highly accurate testing for the detection and quantification of JCPyV DNA with very low limit of detection. This allowed us to shorten turnaround times and save time for technical staff.</p>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"105849"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144804232","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":"Comparison of diagnostic performances of HDV-RNA quantification assays used in clinical practice: Results from a national quality control multicenter study.","authors":"Romina Salpini, Lorenzo Piermatteo, Gian Paolo Caviglia, Ada Bertoli, Maurizia Rossana Brunetto, Bianca Bruzzone, Annapaola Callegaro, Cinzia Caudai, Daniela Cavallone, Luchino Chessa, Fernando Coghe, Nicola Coppola, Nunzia Cuomo, Stefano D'Anna, Mariantonietta Di Stefano, Floriana Facchetti, Claudio Farina, Donatella Ferraro, Elisa Franchin, Daniela Francisci, Silvia Galli, Anna Rosa Garbuglia, William Gennari, Valeria Ghisetti, Pietro Lampertico, Sergio Lo Caputo, Nadia Marascio, Stefano Menzo, Valeria Micheli, Grazia Anna Niro, Antonella Olivero, Pierpaolo Paba, Concetta Ilenia Palermo, Orazio Palmieri, Stefania Paolucci, Mariantonietta Pisaturo, Teresa Pollicino, Giuseppina Raffa, Teresa Santantonio, Giulia Torre, Ombretta Turriziani, Sergio Uzzau, Sara Colonia Uceda Renteria, Marialinda Vatteroni, Maurizio Zazzi, Antonio Craxì, Francesca Ceccherini-Silberstein, Valentina Svicher, Marco Arosio, Sabrina Bastianelli, Annamaria Gentile, Federica A M Giardina, Anna Gidari, Rosalba Govoni, Gabriele Ibba, Alessandro Loglio, Alessandra Lombardi, Chiara Mascarella, Fabrizio Maggi, Giovanni Matera, Chiara Mazzei, Maria Grazia Milia, Angela Quirino, Adriana Raddi, Rosetta Scioscia, Sara Tagliazucchi, Michele Totaro, Rea Valaperta","doi":"10.1016/j.jcv.2025.105850","DOIUrl":"10.1016/j.jcv.2025.105850","url":null,"abstract":"<p><strong>Introduction: </strong>A reliable quantification of hepatitis D virus (HDV) RNA is of paramount importance for monitoring patients under antiviral therapy. This quality control study compares the diagnostic performances of quantitative HDV-RNA assays used in clinical practice.</p><p><strong>Methods: </strong>Two HDV-RNA sample panels were quantified in 30 centers by RoboGene (N = 9 laboratories), EurobioPlex (N = 7), RealStar (N = 4), AltoStar (N = 1), Bosphore (N = 3), Bosphore-on-InGenius (N = 1), Dia.Pro (N = 2), Nuclear-Laser-Medicine (N = 1) and 3 in-house assays. Panel A and B comprised 8 serial dilutions of WHO/HDV standard (range: 0.5-5.0 log10 IU/ml) and 20 clinical samples (range: 0.5-6.0 log10 IU/ml), respectively. The following parameters were determined: sensitivity by 95 % LOD (limit of detection), precision by intra- and inter-run CV (coefficient of variation), accuracy by the differences between expected-observed HDV-RNA, linearity by linear regression analysis.</p><p><strong>Results: </strong>95 % LOD varied across assays and centers underlining heterogeneous sensitivities: AltoStar had the lowest 95 % LOD (3 IU/ml) followed by RealStar (10 [min-max: 3-316] IU/ml), Bosphore-on-InGenius (10 IU/ml), RoboGene (31 [3-316] IU/ml), Nuclear-Laser-Medicine (31 IU/ml) and EuroBioplex (100 [100-316] IU/ml). Moreover, 6 assays (RoboGene, EurobioPlex, RealStar, AltoStar, Nuclear-Laser-Medicine and In-house) showed <0.5 log10 IU/ml differences between expected and observed HDV-RNA for all dilutions while other assays had >1 log10 IU/ml underestimations. RealStar, Bosphore-on-InGenius and EurobioPlex had the highest precision (mean intra-run CV < 20 %). Inter-run CV was higher for all assays, with CVs < 25 % for RealStar, AltoStar, Nuclear-Laser-Medicine and EurobioPlex. Seven assays (RoboGene/AltoStar/RealStar/EurobioPlex/Nuclear-Laser-Medicine/In-house) showed a good linearity (R² > 0.90), but for HDV-RNA < 1000 IU/ml only Bosphore-on-InGenius, AltoStar, RealStar and Robogene showed a R² > 0.85.</p><p><strong>Conclusions: </strong>This study underlines heterogeneous sensitivities (inter- and intraassays), that could hamper proper HDV-RNA quantification, particularly at low viral loads. This raises the need to improve the diagnostic performance of most assays for properly identifying virological response to anti-HDV drugs.</p>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"105850"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144816830","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 Allplex HPV HR Detection assay fulfils international guideline requirements for primary cervical screening on SurePath samples and qualifies as a second-generation HPV comparator test.","authors":"Anja Oštrbenk, Helle Pedersen, Mario Poljak, Jesper Bonde","doi":"10.1016/j.jcv.2025.105853","DOIUrl":"10.1016/j.jcv.2025.105853","url":null,"abstract":"<p><p>A key parameter for the continued success of cervical cancer screening is quality-controlled use of human papillomavirus (HPV) tests that are clinically validated according to international guidelines. The clinical accuracy for cervical screening of the Allplex HPV HR Detection (Allplex), which concurrently detects and distinguishes 12 high-risk HPV types (16,18,31,33,35,39,45,51,52,56,58,59) and HPV66 and HPV68 was assessed on SurePath samples by comparing its performance to the second-generation comparator BD Onclarity HPV assay (Onclarity). The absolute clinical sensitivity, assessed on 76 samples derived from a screening population with underlying CIN2+, of Allplex and Onclarity was 98.7 % (95 % CI, 92.9-100.0 %) and 100.0 % (95 % CI, 95.2-100.0 %), respectively, with relative sensitivity of Allplex of 0.99 (95 % CI; 0.96-1.01). The absolute clinical specificity, assessed on 801 consecutive clinician-collected cervical samples obtained from women 30 to 59 years old attending the routine Danish cervical screening program, for Allplex and Onclarity was 92.5 % (95 % CI, 90.4-94.2 %) and 92.5 % (95 % CI, 90.4-94.2 %), respectively, with relative specificity of Allplex of 1.00 (95 % CI; 0.99-1.01). With thresholds mandated by international guidelines of ≥90 % for relative clinical sensitivity (p = 0.001) and ≥98 % for relative clinical specificity (p = 0.0018), Allplex was non-inferior to Onclarity. Excellent intra- and inter-laboratory agreement of Allplex was observed, both overall (99.2 % and 99.6 %) and at the genotype level (range: 99.6-100.0 %). By fulfilling all guideline requirements for clinical sensitivity, specificity, and reproducibility, Allplex can be considered clinically validated for primary cervical screening using clinician-collected SurePath samples. With this study, Allplex also meets the criteria for a second-generation HPV comparator test.</p>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"180 ","pages":"105853"},"PeriodicalIF":3.4,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144804233","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":"2025-10-01","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":"2025-10-01","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}