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Impact on hospital length of stay and antimicrobial usage in children diagnosed with viral meningitis by rapid multiplexed PCR assay 快速多重聚合酶链反应对诊断为病毒性脑膜炎儿童住院时间和抗菌药物使用的影响
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-08-18 DOI: 10.1016/j.jcv.2025.105856
Jacky Lu , Jessica Flores-Vazquez , Jaehyeon Lee , Leila C. Posch , Cristina Costales , Jennifer Dien Bard
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 < 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).
脑膜炎和脑炎可导致严重的发病率,并导致儿童永久性的神经功能缺损,但结果因致病病原体而异。病毒性脑膜炎的早期诊断可能允许适当的管理,包括避免抗微生物治疗和住院。我们试图确定在一家四级护理儿科机构诊断为人类肠病毒(HEV)和人类parechovirus (HPeV)脑膜炎的患者中多重脑膜炎-脑炎(ME)小组的临床应用。回顾性分析了2016年6月至2023年10月期间由ME小组诊断的HEV或HPeV阳性患者(n = 66)与2011年12月至2016年5月期间通过独立PCR(聚合酶链反应)诊断的HEV或HPeV阳性患者(n = 53)。ME面板的周转时间(TAT)为2.67 h,而独立聚合酶链反应(PCR)的周转时间为22.05 h (p <; 0.0001)。与单独PCR相比,在入院72 h内收集脑脊液(CSF)并进行ME panel检测的患者,静脉注射阿昔洛韦的持续时间显著缩短(3.88 vs 16.03 h, P = 0.03)。尽管采用分子方法检测病毒,但患者仍继续使用抗生素,直到培养48 h后确认脑脊液培养为阴性。在儿科医院实施ME面板提高了病毒性(或无菌性)ME诊断的总体时间。虽然没有统计学意义,但与独立PCR相比,mepanel检测出HEV或HPeV阳性的患者的中位住院时间(LOS)减少了0.51天(1.95天对2.46天,p = 0.66)。
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引用次数: 0
Epstein-Barr virus (EBV) infection and its sequelae in the immunocompetent host eb病毒(EBV)感染及其在免疫活性宿主中的后遗症
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-08-08 DOI: 10.1016/j.jcv.2025.105854
Madeline R. Meirhaeghe , Henry H. Balfour Jr.
Epstein-Barr virus (EBV) is best known as the cause of infectious mononucleosis, which is the most common clinical manifestation of primary EBV infection. Infectious mononucleosis is not a trivial disease, but its importance is overshadowed by the disease burden due to the sequelae of primary EBV infection. This review focuses on the sequelae of EBV infection in the immunocompetent host. These include cancers of lymphoid and epithelial cells, and autoimmune diseases, especially multiple sclerosis (MS).
eb病毒(EBV)被认为是感染性单核细胞增多症的病因,这是原发性EBV感染最常见的临床表现。传染性单核细胞增多症不是一种微不足道的疾病,但它的重要性被由于原发性EBV感染的后遗症所造成的疾病负担所掩盖。本文综述了EBV感染在免疫功能强的宿主中的后遗症。这些包括淋巴细胞癌和上皮细胞癌,以及自身免疫性疾病,尤其是多发性硬化症(MS)。
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引用次数: 0
Evaluation of Cepheid Xpert Xpress CoV-2/Flu/RSV plus for nasal and nasopharyngeal specimens tested in CLIA-accredited and CLIA-waived settings Cepheid Xpert Xpress对在clia认可和放弃clia的环境中检测的鼻和鼻咽标本的CoV-2/Flu/RSV plus的评估
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-08-07 DOI: 10.1016/j.jcv.2025.105851
Erin McElvania , Deepa Rao , Alexander L. Greninger , Glenn Harnett , Allan Larcena , Amrish Patel , Brian Webster , Christina Ulen , Dallas F. Green , Dana King , Deepesh Rubin Patel , Imad Jandali , Jane Gibson , Jennifer Killion , Jibran Atwi , Kelly R. Bergmann , Lance Slade , Mary Allen Staat , Matthew Faron , Megan Washington , Xiaohong Liu

Background

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.

Study design

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.

Results

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.

Conclusions

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.
背景:呼吸道病毒每年导致数百万人就医。2019冠状病毒病的不可预测的周期性以及流感和呼吸道合胞病毒的季节性模式导致这些病毒同时传播,具有非特异性和重叠的临床症状。本研究使用3011份鼻咽拭子(NPS)和2943份前鼻拭子(NS)标本对造父变星Xpert Xpress CoV-2/Flu/RSV plus检测进行了评估。该检测在经过实验室培训的clia认可(CA)实验室和非实验室人员的clia豁免(CW)环境中进行评估。将结果与BioFire Respiratory Panel 2.1检测SARS-CoV-2和Hologic Panther Fusion Flu A/B/RSV检测甲型流感、乙型流感和RSV进行比较。造父变星Xpert Xpress CoV-2/Flu/RSV + NPS和NS标本检测结果与参考检测结果具有高度的阳性和阴性一致性。结果NPS对SARS-CoV-2、甲型流感、乙型流感和RSV的总体符合率分别为98.8%、99.1%、99.9%和100%。对于NS, SARS-CoV-2、甲型流感、乙型流感和RSV的总体一致性分别为98.7%、99.3%、99.9%和99.9%。在CA和CW地点进行的标本测试也与参考测试高度阳性和阴性一致。对于SARS-CoV-2、甲型流感、乙型流感和RSV, CA检测的总体一致性分别为97.7%、99.6%、100%和100%。对于连续波检测,SARS-CoV-2、甲型流感、乙型流感和RSV的总体一致性分别为98.8%、99.0%、99.9%和99.9%。结论本研究表明,无论工作人员是否具有分子检测经验,Xpert Xpress CoV-2/Flu/RSV plus都能在CA和CW检测设施中对NPS和NS标本提供快速准确的结果。
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引用次数: 0
Phylodynamics of human metapneumovirus and evidence for a duplication-deletion model in G gene variant evolution 人偏肺病毒的系统动力学和G基因变异进化中重复-缺失模型的证据
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-08-05 DOI: 10.1016/j.jcv.2025.105848
Stephanie Goya , Ethan B. Nunley , Preston C. Longley , Jamie R. Mathis , Christina G. Varela , Da Yae Kim , Marc Nurik , Samia N. Naccache , Alexander L. Greninger

Background

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.

Study design

We sequenced hMPV genomes from inpatient and outpatient samples collected between 2021 and 2025 in western Washington State and constructed phylogenomic and phylodynamic trees.

Results

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.

Conclusions

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.
2024年12月,随着中国医院病例的增加,人偏肺病毒(hMPV)引起了全球关注,促使世界卫生组织(WHO)发表声明,指出病例数仍在预期范围内。为了评估是否出现了一种公共卫生问题的变体,并检查全球hMPV系统动力学,我们在华盛顿州西部进行了一项基因组监测研究。研究设计:我们对2021年至2025年间在华盛顿州西部收集的住院和门诊患者的hMPV样本进行了基因组测序,并构建了系统基因组和系统动力学树。结果共获得60个hMPV-A基因组和39个hMPV-B基因组,其中13个来自2024年11月至2025年1月。在2019冠状病毒病大流行中断之后,hMPV季节性在2023年之后恢复到典型模式。基因组分析显示,自2022-23年以来hMPV-A优势,与A2b1, A2b2, B1和B2亚谱系共循环。A2b2亚系最为普遍,所有基因组都携带111-nt G基因重复。系统发育证据表明,111-nt变体是通过69-nt的缺失而不是通过独立的重复事件从先前的180-nt重复进化而来的。除A2b1外,大多数亚系表现为多个共循环分支。系统动力学表明,hMPV-A的进化速率高于hMPV-B,在大流行相关的下降之后,全球多样性恢复。没有发现明显的高度关注的进化特征。结论:尽管最近有一些担忧,但我们的研究结果表明,hMPV在美国的传播遵循预期的季节性模式,从先前存在的亚谱系中不断引入不同的病毒变体,而不是出现新的变体。持续的基因组监测至关重要,特别是随着疫苗开发的进展。
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引用次数: 0
Gestational age-dependent dynamics of transplacental CMV and VZV IgG transfer: Weekly comparative analysis in preterm and full-term neonates (24–41 weeks) 经胎盘CMV和VZV IgG转移的胎龄依赖性动力学:早产儿和足月新生儿(24-41周)的每周比较分析
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-08-05 DOI: 10.1016/j.jcv.2025.105847
Niko Kohmer , Clara Seitz-Lüdeke , Thorsten Mosler , Alfred Lennart Bissinger , Ulrich Rochwalsky , Holger F. Rabenau , Horst Buxmann

Background

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.

Methods

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.

Results

Newborn antibody concentrations were significantly lower than maternal levels at 24–29 weeks for both CMV and VZV (p < 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 < 0.05). CMV neutralisation capacity in neonates was significantly lower during weeks 24–29 compared to weeks 30–34 (p < 0.05) and weeks 35–41 (p < 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 < 0.05), and maximum levels in neonates at weeks 35–41 (p < 0.01), indicating enhanced qualitative antibody transfer. Neither gender nor twin-pregnancies showed a significant effect on antibody transfer.

Conclusions

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.
母体IgG抗体经胎盘移植可促进胎儿对巨细胞病毒(CMV)和水痘-带状疱疹病毒(VZV)感染的免疫。关于全胎龄抗体转移的综合数据,特别是在28周之前,仍然有限。方法本前瞻性队列研究分析了n = 564对(孕24-41周)母婴的成对血液样本。采用elisa检测抗巨细胞病毒和抗vzv IgG浓度,采用内部细胞培养法评估巨细胞病毒中和能力。结果新生儿CMV和VZV抗体浓度在24-29周显著低于母体水平(p <;0.05)。CMV在30-34周达到平衡,VZV在30-33周达到平衡。超过35周的巨细胞病毒和34周的VZV,新生儿浓度显著超过母体水平(p <;0.05)。新生儿CMV中和能力在24-29周显著低于30-34周(p <;0.05),第35 ~ 41周(p <;0.01),妊娠期间逐渐改善。母亲的中和能力在整个妊娠期保持不变。新生儿和母亲在中和能力方面的差异是渐进的:在第24-29周最小,在第30-34周显著增加(p <;0.05),而35-41周新生儿的最高水平(p <;0.01),表明定性抗体转移增强。性别和双胎妊娠对抗体转移均无显著影响。结论胎龄依赖性的CMV和VZV IgG抗体转移早在第24周发生。极早产儿表现出明显较低的抗体浓度和CMV中和能力。有针对性的预防策略,为这一弱势群体和进一步的研究,调查具有高中和能力的抗体优先母婴转移是必要的。
{"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}
引用次数: 0
Clinical performance of the BD Onclarity™ HPV extended genotyping assay for anal cancer screening: a prospective pilot study 用于肛门癌筛查的BD Onclarity™HPV扩展基因分型检测的临床表现:一项前瞻性试点研究
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-07-28 DOI: 10.1016/j.jcv.2025.105846
Anna Daniela Iacobone , Fabio Bottari , Davide Radice , Silvia Martella , Pietro Soru , Cristian Mauro , Chiara Scacchi , Clementina Di Tonno , Rita Passerini , Cristina Trovato

Objectives

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.
目的评价扩展HPV基因分型检测在高危人群肛门癌筛查中的临床表现,并调查高危HPV (HR-HPV)基因型在诊断为肛门上皮内瘤变2级或更糟(AIN2+)患者中的流行情况。研究设计一项前瞻性队列研究于2022年9月至2024年9月在意大利米兰的欧洲肿瘤研究所进行。共有202名高风险个体被纳入研究。所有受试者的肛门样本使用ThinPrep PreservCyt毛刷收集,进行HPV检测和基因分型;除非已有组织学资料,否则行细胞学检查。测试了变量与性别之间的关联。计算AIN2+相对于HPV状态的敏感性、特异性和预测值。在总体人群和AIN2+病例中分析HR-HPV基因型患病率。结果无效样本10份,共192人。患者的特征和性别之间没有明显的联系。敏感性、特异性、阳性预测值(PPV)、阴性预测值(NPV)分别为87.7% (95% CI: 76.3-94.9)、72.6% (95% CI: 64.3-79.9)、57.5% (95% CI: 46.4-68.0)、93.3% (95% CI: 86.7-97.3)。大约30%的受试者被诊断为AIN2+。HR-HPV基因型在男女之间分布相似。HPV16在AIN2+病例中占主导地位(70%),其次是女性中的33/58和56/59/66。结论扩展型HPV基因分型可为肛门癌筛查和分类提供潜在的独立工具,从而支持肛门癌筛查策略。需要进一步的研究在更大的队列中证实这些发现。
{"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}
引用次数: 0
SpikeID: Rapid and unbiased identification of SARS-CoV-2 variants by spike sequencing SpikeID:通过刺突测序快速、公正地鉴定SARS-CoV-2变异
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-07-28 DOI: 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.
严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)关注变异体(VOCs)的特征是病毒刺突蛋白S1结构域的不同突变。该结构域包括n端结构域、受体结合结构域和部分裂解位点区域。虽然SARS-CoV-2其他基因组区域的突变会影响VOC潜力,但S1结构域对于识别变体和评估抗原进化和免疫逃逸潜力具有特别重要的意义。方法建立了基于spike S1扩增子测序的快速高通量测序方法SpikeID,用于无偏检测和鉴定SARS-CoV-2变异体。我们对从2021年10月到2024年1月在全球传播的622个临床生物标本进行了SpikeID检测与Illumina全基因组测序的基准测试。结果与全基因组测序相比,spikeid明确检测了100%的who指定voc,并在纽约市(NYC)地区确定了流行率≥1%的PANGO谱系,准确率为93%。这种准确性的降低主要是由于PANGO谱系只能通过S1结构域外的突变来区分。我们证明了SpikeID检测在纽约市出现和随后出现的Omicron和Omicron衍生谱系时的实用性和可扩展性,并表明我们的方法能够经济、可靠和近实时地检测新兴谱系。
{"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}
引用次数: 0
Clinical evaluation of Xpert HIV Qual XC assay in diverse HIV-1 subtypes circulating in China Xpert HIV quality XC检测在中国不同HIV-1亚型流行中的临床评价
IF 3.4 3区 医学 Q2 VIROLOGY Pub Date : 2025-07-26 DOI: 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 ,&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}
引用次数: 0
Emergence of Parechovirus-A5 central nervous system infections in children from Kansas City, Missouri, USA 美国密苏里州堪萨斯城儿童出现Parechovirus-A5中枢神经系统感染
IF 4 3区 医学 Q2 VIROLOGY Pub Date : 2025-07-15 DOI: 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。
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引用次数: 0
The Human Papillomavirus (HPV) Laboratory e-Manual: A comprehensive guide for HPV testing and research 人类乳头瘤病毒(HPV)实验室电子手册:HPV检测和研究的综合指南
IF 4 3区 医学 Q2 VIROLOGY Pub Date : 2025-07-10 DOI: 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.
人类乳头瘤病毒(HPV)疫苗接种和基于HPV的宫颈癌筛查是世界卫生组织(WHO)全球消除宫颈癌战略的中心支柱。世卫组织2009年出版的《人乳头瘤病毒实验室手册》多年来为促进具有国际可比性的人乳头瘤病毒检测质量提供了基本指导。由于这一领域的发展迅速,国家HPV参考实验室全球网络认为有必要更新HPV实验室电子手册,为从事有质量保证的HPV检测研究和/或基于HPV的癌症控制的专业人员提供全面和互动的资源。HPV实验室电子手册涵盖了关键领域,包括实验室质量保证、HPV分类和风险关联、标本收集和处理、核酸提取、HPV检测和分型、HPV血清学、数据管理和国际标准的使用。它提供了最新的协议和最佳做法,以提高HPV检测的准确性和可靠性。交互功能允许实时更新,使其成为全球实验室的动态资源。电子手册由来自11个国家的国际专家编写,其中包括来自国际HPV参考中心(IHRC,瑞典)、疾病预防控制中心全球HPV参考实验室(美国)和多个国家HPV参考实验室(nrl)的贡献者。写一章的标准程序是两个NRL撰写一章,另外一个NRL审核一章。结论HPV实验室电子手册是朝着全球统一HPV检测实验室方法迈出的一步,为研究和宫颈癌控制工作奠定了基础。
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引用次数: 0
期刊
Journal of Clinical Virology
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