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+).
Study design
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.
Results
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 (>70 %), followed by the 33/58 and 56/59/66 pools in women.
Conclusions
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.
{"title":"Clinical performance of the BD Onclarity™ HPV extended genotyping assay for anal cancer screening: a prospective pilot study","authors":"Anna Daniela Iacobone , Fabio Bottari , Davide Radice , Silvia Martella , Pietro Soru , Cristian Mauro , Chiara Scacchi , Clementina Di Tonno , Rita Passerini , 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 (>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}
Pub Date : 2025-07-28DOI: 10.1016/j.jcv.2025.105845
Keith Farrugia , Zain Khalil , Adriana van de Guchte , Bremy Alburquerque , Daniel Floda , PSP Study Group , Komal Srivastava , Luz H. Patiño , Juan David Ramirez , Alberto E. Paniz-Mondolfi , Emilia Mia Sordillo , Viviana Simon , Ana S. Gonzalez-Reiche , Harm van Bakel
Background
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.
Methods
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.
Results
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.
Conclusions
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.
{"title":"SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing","authors":"Keith Farrugia , Zain Khalil , Adriana van de Guchte , Bremy Alburquerque , Daniel Floda , PSP Study Group , Komal Srivastava , Luz H. Patiño , Juan David Ramirez , Alberto E. Paniz-Mondolfi , Emilia Mia Sordillo , Viviana Simon , Ana S. Gonzalez-Reiche , 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}
Pub Date : 2025-07-26DOI: 10.1016/j.jcv.2025.105844
Jiafeng Zhang , Xiaobei Ding , Qin Fan , Xinghui Gao , Mingli Zhu , Wenjie Luo , Yan Xia , Yiwei Tang , Chengliang Chai , Jianmin Jiang
Background
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.
Methods
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.
Results
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 (<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.
Conclusions
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.
背景：早期和准确的HIV-1诊断对于及时开始治疗和预防传播至关重要。本研究评估了Xpert HIV quality XC检测在中国检测不同亚型HIV-1的临床表现。方法：对242份全血进行检测，其中hiv -1阳性215份，阴性15份，非hiv病原体12份。分析了Ct值与log₁0病毒载量之间的敏感性、特异性、kappa系数和相关性。将操作性能与COBAS AmpliPrep/COBAS TaqMan HIV-1定性测试v2.0（简称COBAS系统）在周转时间（TAT）和试剂使用效率方面进行比较。结果：Xpert分析的灵敏度为99.07%，特异性为100.00%，与临床诊断的总体一致性为99.18%。病毒载量不同，检出率也不同，对于病毒载量大于50拷贝/mL的样品，检出率达到100.00%，但对于病毒载量极低的样品，检出率降至84.62%（11/13）。结论：Xpert HIV quality XC检测在不同的HIV-1亚型中表现出色，非常适合分散的诊断环境，支持改进HIV的早期诊断和治疗工作。
{"title":"Clinical evaluation of Xpert HIV Qual XC assay in diverse HIV-1 subtypes circulating in China","authors":"Jiafeng Zhang , Xiaobei Ding , Qin Fan , Xinghui Gao , Mingli Zhu , Wenjie Luo , Yan Xia , Yiwei Tang , Chengliang Chai , 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 (<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}
Pub Date : 2025-07-15DOI: 10.1016/j.jcv.2025.105835
Debarpan Dhar , Anjana Sasidharan , Katelyn E. VanDonge , Brian Lee , Maria Deza-Leon , Christopher J. Harrison , Dithi Banerjee , Rangaraj Selvarangan
Background
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.
Methods
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.
Results
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 (>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.
Conclusions
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.
背景：在美国和全球范围内，小儿麻痹病毒- a5 （PeV-A5）血液和中枢神经系统（CNS）感染是罕见的。我们报告了2024年密苏里州堪萨斯城婴儿中出现的PeV-A5感染。方法作为堪萨斯城儿童慈善医院（CM-KC）护理标准的一部分，于2024年对婴儿脑脊液（CSF）和血液样本进行parechoovirus - a （PeV-A）检测。PeV-A检测包括两步逆转录聚合酶链反应，并使用Sanger测序进行基因分型。我们分析了2024株PeV-A病毒的氨基酸序列和系统发育，并描述了PeV-A感染婴儿的临床特征。结果248例患者的211份脑脊液和46份血液标本中，检出PeV-A感染者10例（4%），其中脑脊液8例，血液2例。9例PeV-A感染患者的病毒分型成功，其中8例为PeV-A5（6例脑脊液，2例血液），1例为PeV-A4（脑脊液）。CM-KC的PeV-A5病毒序列与其他已知的PeV-A5序列聚类，与2018年日本札幌市的PeV-A5病毒序列最相似（> 97%）。CM-KC的PeV-A5检测呈夏秋季季节性。8例PeV-A5感染患者在CM-KC与先前的PeV-A3和PeV-A4感染患者相比，均出现皮疹症状，易激惹性减轻，最高体温降低。结论2024年在美国密苏里州堪萨斯城的婴儿无菌部位（CSF、血液）检测到的PeV-A5是主要的PeV-A基因型，代表了一年内美国婴儿中PeV-A5全系统疾病的最高数量。
{"title":"Emergence of Parechovirus-A5 central nervous system infections in children from Kansas City, Missouri, USA","authors":"Debarpan Dhar , Anjana Sasidharan , Katelyn E. VanDonge , Brian Lee , Maria Deza-Leon , Christopher J. Harrison , Dithi Banerjee , 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 (>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}
Pub Date : 2025-07-10DOI: 10.1016/j.jcv.2025.105834
Laila Sara Arroyo Mühr , Carina Eklund , Camilla Lagheden , Rita Mariel Correa , María Dolores Fellner , Maria Alejandra Picconi , Nazlı Songur , Murat Gultekin , Kate Cuschieri , Jean-Luc Prétet , Quentin Lepiller , Alice Baraquin , Steffi Silling , Kristiane Søreng , Milan Stosic , Gro Kummeneje Presthus , Marc Arbyn , Michael Peeters , Steven Van Gucht , Elizaveta Padalko , Joakim Dillner
Background
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.
Content
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/.
Collaborators
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.
Conclusion
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.
{"title":"The Human Papillomavirus (HPV) Laboratory e-Manual: A comprehensive guide for HPV testing and research","authors":"Laila Sara Arroyo Mühr , Carina Eklund , Camilla Lagheden , Rita Mariel Correa , María Dolores Fellner , Maria Alejandra Picconi , Nazlı Songur , Murat Gultekin , Kate Cuschieri , Jean-Luc Prétet , Quentin Lepiller , Alice Baraquin , Steffi Silling , Kristiane Søreng , Milan Stosic , Gro Kummeneje Presthus , Marc Arbyn , Michael Peeters , Steven Van Gucht , Elizaveta Padalko , 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}
Pub Date : 2025-07-07DOI: 10.1016/j.jcv.2025.105833
Noah Brazer , Venice Servellita , Chengshi Jin , Abiodun Foresythe , Miriam Oseguera , Jenny Nguyen , Nanami Sumimoto , Hee Jae Huh , Andries Feder , Sanchita Bhattacharya , Surabhi Bhaskar , Alicia Sotomayor-Gonzalez , Prachi Saldhi , Chris Choi , Grace X. Li , Komal Gopchandani , Ashley Tippett , Hui-Mien Hsiao , Mark D. Gonzalez , Dalia Gulick , Charles Y. Chiu
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.
{"title":"Differential severity of SARS-CoV-2 variant infections in children and adults with COVID-19","authors":"Noah Brazer , Venice Servellita , Chengshi Jin , Abiodun Foresythe , Miriam Oseguera , Jenny Nguyen , Nanami Sumimoto , Hee Jae Huh , Andries Feder , Sanchita Bhattacharya , Surabhi Bhaskar , Alicia Sotomayor-Gonzalez , Prachi Saldhi , Chris Choi , Grace X. Li , Komal Gopchandani , Ashley Tippett , Hui-Mien Hsiao , Mark D. Gonzalez , Dalia Gulick , 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}
Pub Date : 2025-07-05DOI: 10.1016/j.jcv.2025.105832
Lance D. Presser , Amani Yousef , Elaine McCulloch , Julia Schaumburg , Adam Meijer
Background
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.
Objectives
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).
Results
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 %).
Conclusions
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.
{"title":"Evaluation of molecular detection for respiratory syncytial viruses in World Health Organization Europe region laboratories, 2020–2023","authors":"Lance D. Presser , Amani Yousef , Elaine McCulloch , Julia Schaumburg , 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}
Pub Date : 2025-07-01DOI: 10.1016/j.jcv.2025.105831
Hong Zhang , Jiaqiang Wang , Xiangqin Liu , Xueru Li , Xuexi Zeng , Qing Luo , Jialing Zhong
Immunodeficiency virus (HIV) antigen/antibody screening assays are highly sensitive and specific, but false-positive (FP) results remain a challenge. Understanding the prevalence and factors associated with these FP results is crucial, especially in high HIV burden regions. A retrospective cohort study of 370,291 patients screened with the ARCHITECT HIV Ag/Ab Combo assay at a Sichuan tertiary hospital (January 2022–December 2023) was conducted. We calculated HIV prevalence and assessed the test's FP rate, sensitivity, specificity and positive predictive value (PPV). Clinical characteristics and associated disease profiles of individuals with FP results were also analyzed. The overall HIV infection rate was 0.17 %. The FP rate for HIV screening was 0.08 %, with higher incidences observed among females, children (aged 0–17 years), and individuals aged 66 and older (P < 0.001). The mean signal-to-cutoff ratio (S/CO) in true positives (TPs) was significantly higher than that in FPs (576.63 vs. 1.94, P < 0.0001). A receiver operating characteristic (ROC)-determined cutoff of 19.6 provided optimal sensitivity (95.10 %) and specificity (99.99 %). FP results were associated with 18 disease categories, with digestive system disorders being the most prevalent. Malignant tumors, pregnancy, and cerebral infarction were also linked to FPs. These findings highlight the critical need for targeted screening strategies and more precise interpretation protocols to improve diagnostic accuracy. Furthermore, the link between FP results and various non-HIV-related diseases suggests that careful patient characterization may aid in identifying underlying conditions, thereby informing more effective clinical decision-making and public health interventions.
免疫缺陷病毒（HIV）抗原/抗体筛选测定是高度敏感和特异性的，但假阳性（FP）结果仍然是一个挑战。了解这些计划生育结果的流行情况和相关因素至关重要，特别是在艾滋病毒高负担地区。对四川省某三级医院（2022年1月- 2023年12月）采用ARCHITECT HIV Ag/Ab组合检测筛查的370,291例患者进行回顾性队列研究。我们计算HIV流行率，并评估该检测的FP率、敏感性、特异性和阳性预测值（PPV）。分析了FP结果个体的临床特征和相关疾病概况。总体HIV感染率为0.17%。HIV筛查的计划生育率为0.08%，在女性、儿童（0-17岁）和66岁及以上的人群中发病率较高(P <；0.001)。真阳性（TPs）的平均信号截止比（S/CO）显著高于FPs (576.63 vs. 1.94, P <；0.0001)。受试者工作特征（ROC）确定的截止值为19.6，提供了最佳的灵敏度（95.10%）和特异性（99.99%）。FP结果与18种疾病相关，其中消化系统疾病最为普遍。恶性肿瘤、妊娠和脑梗死也与FPs有关。这些发现强调了有针对性的筛查策略和更精确的解释方案的迫切需要，以提高诊断的准确性。此外，计划生育结果与各种非艾滋病毒相关疾病之间的联系表明，仔细描述患者特征可能有助于确定潜在疾病，从而为更有效的临床决策和公共卫生干预提供信息。
{"title":"False-positive results in fourth-generation HIV screening tests: Prevalence and associated factors in Sichuan, a high HIV burden province of China","authors":"Hong Zhang , Jiaqiang Wang , Xiangqin Liu , Xueru Li , Xuexi Zeng , Qing Luo , Jialing Zhong","doi":"10.1016/j.jcv.2025.105831","DOIUrl":"10.1016/j.jcv.2025.105831","url":null,"abstract":"<div><div>Immunodeficiency virus (HIV) antigen/antibody screening assays are highly sensitive and specific, but false-positive (FP) results remain a challenge. Understanding the prevalence and factors associated with these FP results is crucial, especially in high HIV burden regions. A retrospective cohort study of 370,291 patients screened with the ARCHITECT HIV Ag/Ab Combo assay at a Sichuan tertiary hospital (January 2022–December 2023) was conducted. We calculated HIV prevalence and assessed the test's FP rate, sensitivity, specificity and positive predictive value (PPV). Clinical characteristics and associated disease profiles of individuals with FP results were also analyzed. The overall HIV infection rate was 0.17 %. The FP rate for HIV screening was 0.08 %, with higher incidences observed among females, children (aged 0–17 years), and individuals aged 66 and older (<em>P</em> < 0.001). The mean signal-to-cutoff ratio (S/CO) in true positives (TPs) was significantly higher than that in FPs (576.63 vs. 1.94, <em>P</em> < 0.0001). A receiver operating characteristic (ROC)-determined cutoff of 19.6 provided optimal sensitivity (95.10 %) and specificity (99.99 %). FP results were associated with 18 disease categories, with digestive system disorders being the most prevalent. Malignant tumors, pregnancy, and cerebral infarction were also linked to FPs. These findings highlight the critical need for targeted screening strategies and more precise interpretation protocols to improve diagnostic accuracy. Furthermore, the link between FP results and various non-HIV-related diseases suggests that careful patient characterization may aid in identifying underlying conditions, thereby informing more effective clinical decision-making and public health interventions.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"179 ","pages":"Article 105831"},"PeriodicalIF":4.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144563845","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}
Pub Date : 2025-06-25DOI: 10.1016/j.jcv.2025.105830
Devy M. Emperador , Leanna Sayyad , Monica Brady , Jessica Rowland , Inna Krapiunaya , Isabella Eckerle , Emmanuel Agogo , Daniel G. Bausch , Joel M. Montgomery , John D. Klena
Background
Nucleic acid-based assays are the diagnostic gold standard for filoviruses, including Ebola (EBOV) and Sudan (SUDV) viruses. However, outbreaks in areas with limited laboratory infrastructure highlight the need for simpler diagnostic tests that can be rapidly and safely used in the field.
Methods
We evaluated eight antigen rapid diagnostic tests (Ag-RDTs) for their ability to detect EBOV and SUDV. Analytical panels using virus cell slurries were used to assess limit of detection, and clinical samples were tested to determine sensitivity and specificity.
Results
Five Ag-RDTs detected EBOV and three detected SUDV, although clinical sensitivity was low (20–40 % for EBOV, 33 % for SUDV), improving only with higher viral loads. All assays demonstrated 100 % clinical specificity with no cross-reactivity.
Discussion
Although none of the evaluated Ag-RDTs are suitable for routine diagnosis, some may be useful in high viral load contexts such as cadaver testing. Our findings highlight the need to improve Ag-RDT sensitivity or develop high-sensitivity point-of-care molecular diagnostics.
{"title":"Laboratory evaluation of antigen rapid diagnostic tests to detect Ebola and Sudan viruses","authors":"Devy M. Emperador , Leanna Sayyad , Monica Brady , Jessica Rowland , Inna Krapiunaya , Isabella Eckerle , Emmanuel Agogo , Daniel G. Bausch , Joel M. Montgomery , John D. Klena","doi":"10.1016/j.jcv.2025.105830","DOIUrl":"10.1016/j.jcv.2025.105830","url":null,"abstract":"<div><h3>Background</h3><div>Nucleic acid-based assays are the diagnostic gold standard for filoviruses, including Ebola (EBOV) and Sudan (SUDV) viruses. However, outbreaks in areas with limited laboratory infrastructure highlight the need for simpler diagnostic tests that can be rapidly and safely used in the field.</div></div><div><h3>Methods</h3><div>We evaluated eight antigen rapid diagnostic tests (Ag-RDTs) for their ability to detect EBOV and SUDV. Analytical panels using virus cell slurries were used to assess limit of detection, and clinical samples were tested to determine sensitivity and specificity.</div></div><div><h3>Results</h3><div>Five Ag-RDTs detected EBOV and three detected SUDV, although clinical sensitivity was low (20–40 % for EBOV, 33 % for SUDV), improving only with higher viral loads. All assays demonstrated 100 % clinical specificity with no cross-reactivity.</div></div><div><h3>Discussion</h3><div>Although none of the evaluated Ag-RDTs are suitable for routine diagnosis, some may be useful in high viral load contexts such as cadaver testing. Our findings highlight the need to improve Ag-RDT sensitivity or develop high-sensitivity point-of-care molecular diagnostics.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"179 ","pages":"Article 105830"},"PeriodicalIF":4.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144535129","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":"Corrigendum to “A prospective study of plasma and bronchoalveolar lavage fluid CMV DNA load quantification for the diagnosis and outcome of CMV pneumonitis in immunocompromised hosts” [J. Clin. Virol. 155 (2022) 105243]","authors":"Gasit Saksirisampant , Theerasuk Kawamatawong , Kawin Promsombat , Warawut Sukkasem , Somprasong Liamsombut , Ekawat Pasomsub , Jackrapong Bruminhent","doi":"10.1016/j.jcv.2025.105829","DOIUrl":"10.1016/j.jcv.2025.105829","url":null,"abstract":"","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"179 ","pages":"Article 105829"},"PeriodicalIF":4.0,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484608","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}
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