Journal of Clinical Virology最新文献_第2页

The molecular epidemiology of respiratory syncytial virus in Ontario, Canada from 2022–2024 using a custom whole genome sequencing assay and analytics package 使用定制的全基因组测序测定和分析包研究2022-2024年加拿大安大略省呼吸道合胞病毒的分子流行病学。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2025-02-01 DOI: 10.1016/j.jcv.2024.105759

Henry Wong , Calvin P. Sjaarda , Brittany Rand , Drew Roberts , Kyla Tozer , Ramzi Fattouh , Robert Kozak , Prameet M. Sheth

Background

Respiratory Syncytial Virus (RSV) infections are a cause of significant morbidity and mortality in children and the elderly. Despite the clinical burden of disease, very little is known about the inter- and intra-seasonal genomic variability of RSV. Furthermore, the recent approval of vaccines and monoclonal antibody therapies will likely lead to higher selective pressure on RSV. Genomic surveillance will be essential to monitor viral changes and inform future therapeutic developments and public health responses. Here, we describe the development of an amplicon-based whole-genome sequencing assay for RSV to enable genomic surveillance.

Methods

A 750-bp overlapping amplicon design was developed to co-amplify RSV-A/-B directly from patient samples collected during two respiratory illness seasons (2022/23, 2023/24) for whole-genome sequencing. RSV subtype, clade, and F-protein antigenic site sequences were determined with a custom analytical pipeline.

Results

Of the 429 specimens included in the study 410 (95.6 %) samples met acceptability. Our data demonstrated co-circulation of both RSV subtypes, with increasing predominance of RSV-A since 2022. There were seven genomic clades of RSV-A, while >95 % of RSV-B belonged to a single clade. 1.5 % of samples had amino acid changes within the binding sites of the current RSV therapeutics Palivizumab or Nirsevimab.

Conclusions

Continuous monitoring of RSV genotypes and mutations will be critical for understanding the impact of new therapeutics and vaccines on RSV epidemiology and detecting emergence of vaccine-escape and/or antiviral resistant mutations.

背景：呼吸道合胞病毒（RSV）感染是儿童和老年人发病和死亡的重要原因。尽管存在疾病的临床负担，但对RSV的季节间和季节内基因组变异性知之甚少。此外，最近批准的疫苗和单克隆抗体疗法可能会导致对RSV的更高选择压力。基因组监测对于监测病毒变化和为未来的治疗发展和公共卫生反应提供信息至关重要。在这里，我们描述了基于扩增子的RSV全基因组测序测定的发展，以实现基因组监测。方法：建立750 bp重叠扩增子设计，直接从两个呼吸道疾病季节（2022/23和2023/24）收集的患者样本中共扩增RSV-A/-B，用于全基因组测序。RSV亚型、进化支和f蛋白抗原位点序列用定制的分析管道测定。结果：纳入研究的429份样本中，410份（95.6%）样本符合可接受性。我们的数据显示两种RSV亚型共循环，自2022年以来RSV- a的优势越来越大。RSV-A有7个基因组分支，而RSV-B有95%属于单一分支。1.5%的样本在当前RSV治疗药物帕利维珠单抗或尼瑟维单抗的结合位点有氨基酸变化。结论：持续监测RSV基因型和突变对于了解新疗法和疫苗对RSV流行病学的影响以及检测疫苗逃逸和/或抗病毒耐药突变的出现至关重要。

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引用次数: 0

Nucleic acid amplification testing using dried blood spots to confirm the diagnosis of HIV-1 in adults 使用干血斑进行核酸扩增检测，以确诊成人是否感染 HIV-1。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-11-17 DOI: 10.1016/j.jcv.2024.105746

Benjamin A. Pinsky , Malaya K. Sahoo , Justen Manasa , Tariro Makadzange , Carole L. Wallis , Ed G. Marins , Nagalingeswaran Kumarasamy , John A. Bartlett , Ronald J. Bosch , Dennis Israelski , David A. Katzenstein , A5230 and PARC teams

Background

The WHO HIV testing algorithm for high prevalence populations recommends the use of three different serologic assays, though this approach may lead to diagnostic misclassification. The study objective was to compare dried blood spot (DBS)-based HIV-1 nucleic acid detection methods to determine their suitability to confirm the diagnosis of HIV-1 in adults generally with suppressed or low-level plasma HIV-1 RNA.

Methods

Four methods were evaluated: Cepheid Xpert HIV-1 Qual Assay (Xpert), Hologic Aptima HIV-1 Quant Dx assay (Aptima), Roche Cobas Ampliprep/Cobas TaqMan HIV-1 test, v.2.0 (CAP/CTM) with guanidinium-based sample pre-extraction buffer (SPEX), or CAP/CTM with phosphate-buffered saline (PBS). Testing was performed on 163 DBS samples collected from participants with HIV-1 in the AIDS Clinical Trial Group (ACTG) A5230 study (73 samples) and the Peninsula AIDS Research Cohort (PARC) study (90 samples).

Results

Xpert and SPEX CAP/CTM [96.9 % (158/163):95.7 % (156/163); P = 0.75) showed similar sensitivity. However, PBS CAP/CTM and Aptima demonstrated significantly lower sensitivity, 68.2 % (107/157) and 69.2 % (99/143), respectively, compared to Xpert and SPEX CAP/CTM (P < 0.0001 for all comparisons). Overall agreement between Xpert and SPEX CAP/CTM was 93.9 % (153/163), including 152 DBS samples in which both methods detected HIV-1 nucleic acids.

Conclusions

Xpert and SPEX CAP/CTM provide sensitive performance for the detection of HIV-1 nucleic acids using DBS collected from adults living with HIV-1, including those with suppressed virus loads. Given the cost and side-effects associated with inappropriate life-long antiretroviral therapy, these assays may play a role in diagnosing HIV-1 infection in individuals with suspected false-positive serologic testing.

背景：世界卫生组织针对高发人群的艾滋病检测算法建议使用三种不同的血清学检测方法，但这种方法可能会导致诊断分类错误。本研究的目的是比较基于干血斑（DBS）的 HIV-1 核酸检测方法，以确定这些方法是否适合用于确诊血浆 HIV-1 RNA 一般处于抑制或低水平的成人的 HIV-1：方法：对四种方法进行了评估：方法：对四种方法进行了评估：Cepheid Xpert HIV-1 Qual Assay (Xpert)、Hologic Aptima HIV-1 Quant Dx assay (Aptima)、Roche Cobas Ampliprep/Cobas TaqMan HIV-1 test, v.2.0 (CAP/CTM)与胍基样品预提取缓冲液 (SPEX) 或 CAP/CTM 与磷酸盐缓冲盐水 (PBS)。我们对从艾滋病临床试验小组（ACTG）A5230 研究（73 个样本）和半岛艾滋病研究队列（PARC）研究（90 个样本）的 HIV-1 参与者身上采集的 163 份 DBS 样本进行了检测：Xpert 和 SPEX CAP/CTM [96.9 % (158/163):95.7 % (156/163); P = 0.75]显示出相似的灵敏度。然而，与 Xpert 和 SPEX CAP/CTM 相比，PBS CAP/CTM 和 Aptima 的灵敏度明显较低，分别为 68.2 % (107/157) 和 69.2 % (99/143)（所有比较中 P < 0.0001）。Xpert和SPEX CAP/CTM的总体一致性为93.9%（153/163），其中152份DBS样本中两种方法都检测到了HIV-1核酸：结论：Xpert 和 SPEX CAP/CTM 在使用从成年 HIV-1 感染者（包括病毒载量受到抑制者）采集的 DBS 检测 HIV-1 核酸方面具有灵敏的性能。考虑到不适当的终身抗逆转录病毒疗法所带来的成本和副作用，这些检测方法可在诊断血清学检测假阳性的 HIV-1 感染者时发挥作用。

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引用次数: 0

Quantification of human immunodeficiency virus type 2 (HIV-2) viral load in plasma: Comparison of three commercial assays 血浆中人体免疫缺陷病毒 2 型（HIV-2）病毒载量的定量：三种商业检测方法的比较。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-11-12 DOI: 10.1016/j.jcv.2024.105745

Iker Falces-Romero , Isabel García-Pérez , Luz Martín-Carbonero , Julio García-Rodríguez , Jesús Mingorance

Introduction

There are few validated commercially available HIV-2 assays for the measurement of viral load. Our aim was to compare three commercial assays for the quantification of HIV-2 viral load in plasma of patients with HIV-2 infection from our hospital.

Material and methods

We conducted a retrospective study at our tertiary-care hospital, analyzing samples from patients with known HIV-2 infection collected between 2022 and 2023. We compared three commercial assays for quantification of the viral load, Biomérieux® NASBA assay, Thermo Fisher® digital PCR (dPCR) assay and Altona® RT-PCR assay.

Results

A total of 27 samples from 11 different patients were included in the study. Sixteen out of them were negative across all three assays. One sample had a low viral load (<2 log copies/mL) detected by the three assays. In five samples a low viral load was only detected by the Altona® assay. The remaining five samples, all from the same patient infected by a multidrug-resistant HIV-2, showed detectable viral load up to 2 log copies/mL by the Thermo Fisher® and Altona® assays, but none of these samples were detected by the Biomérieux® assay.

Conclusions

The Altona® RT-PCR assay and the ThermoFisher® dPCR assay could be reliable options as commercial assays for the quantification of HIV-2 RNA in plasma. However, the Biomérieux® NASBA assay, despite detecting both HIV-1 and HIV-2, may have limitations for HIV-2 detection in some cases.

导言：目前市场上几乎没有经过验证的用于检测病毒载量的 HIV-2 检测方法。我们的目的是比较三种用于定量检测本医院 HIV-2 感染者血浆中 HIV-2 病毒载量的商用检测方法：我们在我们的三级医院进行了一项回顾性研究，分析了 2022 年至 2023 年间收集的已知 HIV-2 感染者的样本。我们比较了生物梅里埃® NASBA 检测法、赛默飞世尔® 数字 PCR (dPCR) 检测法和 Altona® RT-PCR 检测法这三种用于量化病毒载量的商业检测法：研究共纳入了来自 11 位不同患者的 27 份样本。其中 16 份样本的三种检测结果均为阴性。其中一份样本的病毒载量较低（结论：Altona® RT-PCR 检测方法的病毒载量较低）：Altona® RT-PCR 检测法和 ThermoFisher® dPCR 检测法是血浆中 HIV-2 RNA 定量的可靠商用检测法。然而，Biomérieux® NASBA 检测试剂盒虽然可以检测 HIV-1 和 HIV-2，但在某些情况下对 HIV-2 的检测可能存在局限性。

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引用次数: 0

Coinfections and iterative detection of respiratory viruses among 17,689 patients between March 2021 and December 2022 in Southern France 2021 年 3 月至 2022 年 12 月期间法国南部 17689 名患者的合并感染和呼吸道病毒迭代检测。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-11-07 DOI: 10.1016/j.jcv.2024.105744

Cédric Mantelli , Philippe Colson , Lucile Lesage , Didier Stoupan , Hervé Chaudet , Aurélie Morand , Bernard La Scola , Céline Boschi

Objectives

We aimed to describe coinfections and iterative infections with respiratory viruses diagnosed over a 22-month period in 2021–2022 in public university hospitals of the second largest French city.

Material and methods

Respiratory virus infections were diagnosed by qPCR with the Fast Track Diagnostics Respiratory Pathogens 21 on nasopharyngeal swabs collected between 01/03/2021–31/10/2022 and sent for routine diagnosis purpose to our clinical microbiology-virology laboratory at public university hospitals of Marseille, Southern France.

Results

Nasopharyngeal swabs from 17,689 patients were tested, of which 8,133 (46 %) were positive for ≥1 respiratory virus and 1,255 (15%) were co-infected with ≥2 viruses including 213 (2.6 %) with 3–7 viruses. Among them, 1,005 (80 %) were younger than 5 years, and mean age was significantly lower for coinfected than monoinfected patients (6.6 versus 23.8 years; p < 0.0001). Viruses with the highest confection rates were HBoV (97 %), HPeV (97 %), EV (92 %), ADV (68 %), and HCoV-HKU1 (63 %). Iterative infections were observed in 96 patients and they involved 10 different viruses.

Conclusions

Our study points out that coinfections with respiratory viruses vary over time in prevalence, involve majoritarily young children, and may involve concurrent acute infections or acute-on-chronic infections, which deserves further specific studies.

目的我们旨在描述法国第二大城市公立大学医院在2021-2022年22个月期间诊断出的呼吸道病毒并发感染和重复感染：对2021年3月1日至2022年10月31日期间采集的鼻咽拭子进行qPCR检测，诊断呼吸道病毒感染，并将其送至法国南部马赛公立大学医院临床微生物学-病毒学实验室进行常规诊断：检测了 17,689 名患者的鼻咽拭子，其中 8,133 人（46%）对≥1 种呼吸道病毒呈阳性，1,255 人（15%）合并感染了≥2 种病毒，包括 213 人（2.6%）感染了 3-7 种病毒。其中 1 005 人（80%）的年龄小于 5 岁，合并感染者的平均年龄明显低于单一感染者（6.6 岁对 23.8 岁；P < 0.0001）。感染率最高的病毒是 HBoV（97%）、HPeV（97%）、EV（92%）、ADV（68%）和 HCoV-HKU1（63%）。在 96 名患者中观察到了迭代感染，涉及 10 种不同的病毒：我们的研究指出，呼吸道病毒合并感染的发病率随时间而变化，主要涉及幼儿，并可能涉及并发急性感染或急性合并慢性感染，值得进一步开展具体研究。

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引用次数: 0

Performance evaluation of the Abbott Alinity Hepatitis C antigen next assay in a US urban emergency department population 雅培 Alinity 丙型肝炎抗原下一步测定在美国城市急诊科人群中的性能评估。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-30 DOI: 10.1016/j.jcv.2024.105743

John Prostko , Richard Rothman , Yu-Hsiang Hsieh , Sandra Pearce , Mark Kilbane , Karl McAuley , Edwin Frias , Russell Taylor , Hussain Ali , Carsten Buenning , Jessica Grieshaber , Jenna Bedrava , David Daghfal

Introduction

HCV antibody assays have been used to screen for HCV, but confirmation of acute infection is dependent on RNA or core antigen testing. The aim of the study was to compare the performance of five HCV test methods, including RNA testing, on a US emergency department population.

Methods

Clinical performance metrics were calculated on 708 consenting Johns Hopkins Emergency Department patients who self-reported an increased risk for HCV infection. Detection times of antibody, antigen, and RNA testing were compared using 89 samples from commercially available seroconversion panels. Testing was performed on the Abbott Alinity HCV Ag Next (RUO), Roche Elecsys HCV Duo, Abbott ARCHITECT Anti-HCV, and Elecsys Anti-HCV II assays. RNA testing was performed on the Abbott m2000 system.

Results

Overall, 21 (3.0%) participants tested positive for HCV on at least one test, 11 (52.4%) had chronic, 1 (4.8%) had an acute, and 3 (14.3%) had resolved infections. The Alinity HCV Ag Next assay demonstrated 99.43% specificity when compared to RNA testing. The Alinity HCV Ag Next assay also detected 91.67% of the active infections compared to RNA testing, while the Elecsys HCV Duo Ag assay detected only 58.33%. The seroconversion panel testing demonstrated that the Alinity HCV Ag Next assay detects an infection within 0.8 days of an RNA result.

Conclusion

The Alinity HCV Ag Next assay demonstrated excellent concordance to RNA testing in a US urban E.D. population. This data supports the utility of Alinity HCV Ag Next in diagnosis of active HCV infections.

导言：HCV抗体检测已被用于筛查HCV，但急性感染的确诊则依赖于RNA或核心抗原检测。本研究的目的是在美国急诊科人群中比较包括 RNA 检测在内的五种 HCV 检测方法的性能：方法：对约翰霍普金斯大学急诊科的 708 名自述感染 HCV 风险增高并征得同意的患者计算临床性能指标。使用 89 份来自市售血清转换面板的样本比较了抗体、抗原和 RNA 检测的检测时间。雅培 Alinity HCV Ag Next (RUO)、罗氏 Elecsys HCV Duo、雅培 ARCHITECT Anti-HCV 和 Elecsys Anti-HCV II 分析仪进行了检测。RNA 检测在雅培 m2000 系统上进行：总体而言，21 名参与者（3.0%）至少有一次检测结果呈 HCV 阳性，其中 11 人（52.4%）为慢性感染，1 人（4.8%）为急性感染，3 人（14.3%）为已解决感染。Alinity HCV Ag Next 检测法与 RNA 检测法相比，特异性高达 99.43%。与 RNA 检测相比，Alinity HCV Ag Next 检测法还能检测出 91.67% 的活动感染，而 Elecsys HCV Duo Ag 检测法只能检测出 58.33%。血清转换面板检测表明，Alinity HCV Ag Next 检测试剂盒能在 RNA 检测结果出来后的 0.8 天内检测出感染：结论：Alinity HCV Ag Next 检测法与 RNA 检测法在美国城市 E.D.Population 中的一致性非常好：这些数据支持 Alinity HCV Ag Next 在诊断活动性 HCV 感染中的实用性。

{"title":"Performance evaluation of the Abbott Alinity Hepatitis C antigen next assay in a US urban emergency department population","authors":"John Prostko , Richard Rothman , Yu-Hsiang Hsieh , Sandra Pearce , Mark Kilbane , Karl McAuley , Edwin Frias , Russell Taylor , Hussain Ali , Carsten Buenning , Jessica Grieshaber , Jenna Bedrava , David Daghfal","doi":"10.1016/j.jcv.2024.105743","DOIUrl":"10.1016/j.jcv.2024.105743","url":null,"abstract":"<div><h3>Introduction</h3><div>HCV antibody assays have been used to screen for HCV, but confirmation of acute infection is dependent on RNA or core antigen testing. The aim of the study was to compare the performance of five HCV test methods, including RNA testing, on a US emergency department population.</div></div><div><h3>Methods</h3><div>Clinical performance metrics were calculated on 708 consenting Johns Hopkins Emergency Department patients who self-reported an increased risk for HCV infection. Detection times of antibody, antigen, and RNA testing were compared using 89 samples from commercially available seroconversion panels. Testing was performed on the Abbott Alinity HCV Ag Next (RUO), Roche Elecsys HCV Duo, Abbott ARCHITECT Anti-HCV, and Elecsys Anti-HCV II assays. RNA testing was performed on the Abbott m2000 system.</div></div><div><h3>Results</h3><div>Overall, 21 (3.0%) participants tested positive for HCV on at least one test, 11 (52.4%) had chronic, 1 (4.8%) had an acute, and 3 (14.3%) had resolved infections. The Alinity HCV Ag Next assay demonstrated 99.43% specificity when compared to RNA testing. The Alinity HCV Ag Next assay also detected 91.67% of the active infections compared to RNA testing, while the Elecsys HCV Duo Ag assay detected only 58.33%. The seroconversion panel testing demonstrated that the Alinity HCV Ag Next assay detects an infection within 0.8 days of an RNA result.</div></div><div><h3>Conclusion</h3><div>The Alinity HCV Ag Next assay demonstrated excellent concordance to RNA testing in a US urban E.D. population. This data supports the utility of Alinity HCV Ag Next in diagnosis of active HCV infections.</div></div>","PeriodicalId":15517,"journal":{"name":"Journal of Clinical Virology","volume":"175 ","pages":"Article 105743"},"PeriodicalIF":4.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142568010","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}

引用次数: 0

Standardization and evaluation of an in-house ELISA for the detection of rabies antibody in a tertiary care centre in South India 印度南部一家三级医疗中心用于检测狂犬病抗体的内部酶联免疫吸附试验的标准化和评估

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-28 DOI: 10.1016/j.jcv.2024.105742

Kalpana Thangavelu, Hubert D-J Daniel, Rajesh Kannangai, Asha Mary Abraham, Selva Kumar Velladurai, Dr. Shoba Mammen

Background

Rapid fluorescent focus inhibition test (RFFIT), a neutralization-based assay for detecting rabies antibodies, is the gold standard. The National Action Plan for Dog Mediated Rabies Elimination (NAPRE) is a national program that strategizes the establishment of enzyme-linked immunosorbent assays (ELISA) to detect rabies antibodies.

Objective

We developed an in-house ELISA to screen for rabies antibodies using rabies vaccine antigen to study vaccine response among health care workers (HCWs) who received pre-exposure prophylaxis and a few animal bite victims who received post-exposure prophylaxis with rabies vaccine.

Study design

A prospective study was carried out from April to September 2023 at the Department of Clinical Virology of a tertiary care center in South India. A total of 161 serum specimens, which included 155 serum samples from study participants and 6 samples from a reference laboratory (as controls), were obtained during the study period. Rabies antibody was determined by the in-house standardized ELISA developed using the rabies vaccine and compared with the reference assay, RFFIT. The accuracy indices of the in-house ELISA were estimated by MedCalc software (version 22.023).

Results

A panel of 86 positive and 75 negative serum samples was used for evaluating the in-house standardized ELISA. The sensitivity, specificity, positive and negative predictive values of the in-house ELISA were 98.8 %, 100 %, 100 %, and 98.7 % respectively. The accuracy of the in-house ELISA is 99.4 %.

Conclusion

ELISA can be a practically feasible and less expensive assay compared to RFFIT which is a cumbersome procedure with a long turn-around time of 3–4 days.

背景快速荧光聚焦抑制试验（RFFIT）是一种基于中和的狂犬病抗体检测方法，是检测狂犬病抗体的黄金标准。消灭犬媒狂犬病国家行动计划（NAPRE）是一项国家计划，其战略是建立酶联免疫吸附试验（ELISA）来检测狂犬病抗体。研究设计 2023 年 4 月至 9 月，南印度一家三级医疗中心的临床病毒学部门开展了一项前瞻性研究。研究期间共采集了 161 份血清样本，其中 155 份来自研究参与者，6 份来自参考实验室（作为对照）。狂犬病抗体通过使用狂犬病疫苗开发的内部标准化酶联免疫吸附测定法进行测定，并与参考测定法 RFFIT 进行比较。用 MedCalc 软件（22.023 版）估算了内部 ELISA 的准确性指数。内部 ELISA 的灵敏度、特异性、阳性预测值和阴性预测值分别为 98.8%、100%、100% 和 98.7%。内部 ELISA 的准确率为 99.4%。结论 ELISA 与 RFFIT 相比，是一种实际可行且成本较低的检测方法，后者程序繁琐，周转时间长达 3-4 天。

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引用次数: 0

Detection of yellow fever virus genome in urine following natural infection or vaccination: review of current knowledge 1985–2023. 自然感染或接种疫苗后尿液中黄热病病毒基因组的检测：1985-2023 年现有知识回顾。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-24 DOI: 10.1016/j.jcv.2024.105740

Zsofia Igloi , Laura Pezzi , Remi N. Charrel , Marion Koopmans

Background

Yellow fever virus (YFV) is endemic in the (sub)tropical regions of Africa and South America and is prone to cause epidemics. Molecular testing of YFV by reverse transcription-polymerase chain reaction (RT-PCR) was recently adopted by WHO using blood. Urine is a non-invasive diagnostic specimen which has been proven to be useful in diagnosing several flavivirus infections. Until now, systematic data on the usefulness of urine in YFV molecular diagnostics was lacking.

Methods

We have carried out an extensive literature search using key words “yellow fever AND urine” in PubMed/Medline, Embase and Web of Science.

Results

The search resulted initially in 113 publications. All titles and abstracts were screened and 15 were analyzed in detail. After natural infection (10 articles), the detection ratio of YFV in blood with RT-PCR was 61 % (105/171 samples) vs. 59 % (139/234) in urine from patients with mild/severe infections. YFV could be first detected at average 4.3 days in blood vs. 6.1 days in urine and last detected till 17.2 vs. 31.1 days respectively (significant difference p < 0.05). Viral load over time in blood was not statistically different from urine. Virus could be isolated from blood, urine and semen. Following vaccination, virus was detected longer in patients with vaccine adverse events (VAE) compared to healthy vaccinees (average 34 vs. 25 days, not significant p > 0.05).

Conclusion

YFV can be detected in urine later but longer. Thus, we see added value for YF molecular diagnostics and sequencing and recommend it besides blood as a standard specimen, especially for late samples post onset.

背景黄热病病毒（YFV）是非洲和南美洲（亚）热带地区的地方病，容易引发流行病。世卫组织最近采用血液通过反转录聚合酶链反应（RT-PCR）对黄热病病毒进行分子检测。尿液是一种非侵入性诊断样本，已被证明可用于诊断多种黄病毒感染。到目前为止，还缺乏关于尿液在黄热病病毒分子诊断中的作用的系统数据。方法我们在 PubMed/Medline、Embase 和 Web of Science 中使用关键词 "黄热病和尿液 "进行了广泛的文献检索。对所有标题和摘要进行了筛选，并对 15 篇文章进行了详细分析。自然感染后（10 篇文章），用 RT-PCR 法检测血液中 YFV 的比例为 61%（105/171 个样本），而检测轻度/重度感染患者尿液中 YFV 的比例为 59%（139/234 个样本）。血液中首次检测到 YFV 的平均时间为 4.3 天，而尿液中为 6.1 天；最后检测到 YFV 的平均时间为 17.2 天，而尿液中为 31.1 天（显著差异 p <0.05）。血液中的病毒载量与尿液中的病毒载量没有统计学差异。病毒可从血液、尿液和精液中分离出来。接种疫苗后，与健康接种者相比，疫苗不良事件（VAE）患者检测到病毒的时间更长（平均 34 天对 25 天，差异不显著 p > 0.05）。因此，我们认为 YF 分子诊断和测序具有附加值，建议除血液外将其作为标准样本，尤其是发病后的晚期样本。

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引用次数: 0

Clinical accuracy of OncoPredict HPV Quantitative Typing (QT) assay on self-samples OncoPredict HPV 定量分型 (QT) 分析法在自采样本上的临床准确性

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-21 DOI: 10.1016/j.jcv.2024.105737

Ardashel Latsuzbaia , Marianna Martinelli , Chiara Giubbi , Kate Cuschieri , Hana Elasifer , Anna D. Iacobone , Fabio Bottari , Andrea F. Piana , Roberto Pietri , Giancarlo Tisi , Franco Odicino , Clementina E. Cocuzza , Marc Arbyn , European VALHUDES working group

Background

The VALHUDES initiative was established to assess the clinical accuracy of HPV assays to detect cervical precancers using urine and vaginal self-samples compared to cervical clinician-collected samples. Here, the clinical performance of OncoPredict HPV Quantitative Typing (QT) assay (OncoPredict QT) was evaluated.

Methods

490 women referred to colposcopy self-collected a urine and a vaginal specimen using Colli-Pee and FLOQSwab, respectively. Subsequently, a colposcopy was performed, and a cervical sample was collected with Cervex-Brush, followed by biopsy if clinically indicated. Vaginal samples were transported dry and resuspended in 5 mL of eNAT medium, whilst cervical brushings were immediately transferred in 20 mL ThinPrep.

Results

The clinical sensitivity of OncoPredict HPV QT testing for CIN2+ in urine and vaginal self-samples was similar to cervical samples (ratios of 0.99 [95 % CI 0.94–1.05] and 1.00 [95 % CI 0.96–1.04]), respectively, when manufacturer's cut-offs were applied. The specificity for <CIN2 on both self-samples was lower than on cervical samples (urine/cervical ratio = 0.91 [95 % CI 0.84–0.98]; vaginal/cervical ratio = 0.90 [95 % CI 0.84–0.98]). Cut-off optimisation improved specificity without compromising sensitivity. Median viral load values adjusted for cellularity were significantly higher in cervical samples compared to urine or vaginal self-samples, in general for all 12 high-risk HPV and in particular for HPV16, 18, 31, 33, 35, 45, 51, 58 (p < 0.05). No difference was observed in median viral loads between urine and vaginal samples.

Conclusion

Following cut-off optimisation OncoPredict HPV QT assay demonstrated similar accuracy on self-collected versus cervical samples.

背景VALHUDES计划旨在评估使用尿液和阴道自取样本检测宫颈癌前病变的HPV测定与宫颈临床医生采集样本相比的临床准确性。方法 490 名转诊至阴道镜检查的妇女分别使用 Colli-Pee 和 FLOQSwab 自取了尿液和阴道样本。随后进行阴道镜检查，用 Cervex-Brush 采集宫颈样本，如有临床指征则进行活检。结果当采用制造商的临界值时，OncoPredict HPV QT 检测尿液和阴道自取样本中 CIN2+ 的临床灵敏度与宫颈样本相似（比率分别为 0.99 [95 % CI 0.94-1.05] 和 1.00 [95 % CI 0.96-1.04]）。两种自检样本的<CIN2特异性均低于宫颈样本（尿液/宫颈比值=0.91 [95 % CI 0.84-0.98]；阴道/宫颈比值=0.90 [95 % CI 0.84-0.98]）。临界值优化提高了特异性，但并不影响灵敏度。与尿液或阴道自检样本相比，宫颈样本经细胞调整后的病毒载量中位值明显较高，一般来说，所有 12 种高风险 HPV 都是如此，尤其是 HPV16、18、31、33、35、45、51 和 58（p <0.05）。尿液样本和阴道样本的病毒载量中位数没有差异。结论经过截断点优化后，OncoPredict HPV QT 检测法在自取样本和宫颈样本中显示出相似的准确性。

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引用次数: 0

International external quality assessment study for detection of monkeypox virus by PCR supporting laboratory preparedness during the 2022–2023 mpox outbreak and beyond 通过 PCR 检测猴痘病毒的国际外部质量评估研究，支持实验室在 2022-2023 年猴痘爆发期间及以后做好准备。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-21 DOI: 10.1016/j.jcv.2024.105741

Rosina Ehmann , Oliver Donoso Mantke , Elaine McCulloch , Amani Yousef , Alastair Ricketts , Harry Staines , Joachim J. Bugert , Roman Wölfel , Hubert G.M. Niesters

Background

Diagnostic capabilities and correspondent External Quality Assessments (EQA) are key for outbreak preparedness. To support diagnostic facilities with a quality assessment of newly established monkeypox virus (MPXV) molecular diagnostic workflows, Quality Control for Molecular Diagnostics (QCMD) and the Bundeswehr Institute of Microbiology (IMB) piloted an international EQA study conducting four challenges from autumn 2022 to summer 2023 during the global mpox outbreak.

Objectives

To assess the performance (sensitivity/specificity) of molecular assays used by diagnostic laboratories.

Study design

Inactivated EQA panels were prepared and distributed containing seven samples of clade Ia and clade IIb MPXV strains at different viral concentrations, two specificity controls with other zoonotic orthopoxviruses (vaccinia and cowpox virus) and a negative control. Assessment was based on reported qualitative testing results.

Results

In this outbreak-related EQA study, a total of 192 laboratories from 37 countries reported 346 qualitative datasets. Overall, core samples were correctly detected by approximately 92 % of participants in all four challenges. While sensitivity performance was acceptable in at least 90 % of datasets correctly reported even for educational MPXV-positive samples with low viral concentration [10² genome equivalents (GE)/mL], several laboratories reported the educational specificity controls as false positives or were unable to differentiate MPXV from related orthopoxviruses.

Conclusions

Mpox is now a globally occurring infection with a demand for quality-assured diagnostic capabilities. The newly established EQA scheme presented here, offers a multi-purpose panel for orthopoxviruses with a focus on MPXV which will continue to ensure diagnostic quality in clinical settings with up-to-date sample panels.

背景：诊断能力和相应的外部质量评估（EQA）是防范疫情爆发的关键。为支持诊断机构对新建立的猴痘病毒（MPXV）分子诊断工作流程进行质量评估，分子诊断质量控制中心（QCMD）和德国联邦国防军微生物研究所（IMB）在2022年秋季至2023年夏季全球猴痘疫情暴发期间开展了一项国际外部质量评估试点研究，进行了四次挑战：评估诊断实验室使用的分子检测方法的性能（灵敏度/特异性）：研究设计：制备并分发了灭活的 EQA 面板，其中包含七份不同病毒浓度的 Ia 支和 IIb 支 MPXV 株样本、两份含有其他人畜共患病正痘病毒（疫苗和牛痘病毒）的特异性对照和一份阴性对照。评估基于报告的定性检测结果：在这项与疫情相关的 EQA 研究中，共有来自 37 个国家的 192 个实验室报告了 346 个定性数据集。总体而言，在所有四项挑战中，约 92% 的参与者都能正确检测出核心样本。即使是病毒浓度较低的MPXV阳性教育样本[102基因组当量（GE）/毫升]，至少有90%的数据集报告正确，灵敏度表现尚可接受，但一些实验室报告的教育特异性对照为假阳性，或无法将MPXV与相关正痘病毒区分开来：结论：MPXV 现已成为一种全球性感染，需要有质量保证的诊断能力。本文介绍的新建立的 EQA 计划提供了一个以 MPXV 为重点的骨痘病毒多用途样本库，它将继续确保临床环境中最新样本库的诊断质量。

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引用次数: 0

Validation, implementation and quality control of a Torque Teno Virus qPCR in a multinational clinical trial 在一项跨国临床试验中验证、实施和控制 Torque Teno 病毒 qPCR。

IF 4 3区医学 Q2 VIROLOGY

Journal of Clinical Virology

Pub Date : 2024-10-16 DOI: 10.1016/j.jcv.2024.105738

E.J. Gore , L. Gard , P. Bourgeois , D. Kulifaj , E. McCulloch , P.G. Spezia , H.G.M. Niesters , F. Maggi , G. Bond , C. Van Leer-Buter , TTVguideTX consortium partners

Background

Immunosuppressive medication after organ transplantation is usually dosed through therapeutic drug monitoring. Trough levels of antirejection medication however, do not adequately predict rejection or infections. The TTVguideIT trial is a multinational clinical trial evaluating the safety of Torque Teno Virus (TTV) load assessed by qPCR, as an alternative to trough level tacrolimus dosing.

Methods

Prior to, and during the clinical trial, the inter-and intra-laboratory variability, accuracy, and precision of the TTV R-GENE® assay was evaluated through analysis of internal quality control (IQC), external quality assessment (EQA) and linearity panels performed by the thirteen participating clinical virology laboratories, each using their standard testing platforms.

Results

IQC samples with a target of 4 log₁₀ copies/mL (cp/mL) were tested by the participating laboratories 130 times during the implementation phase and 987 times during the trial phase. They showed excellent accuracy, with an inter-laboratory standard deviation (SD) of 0.17 log₁₀ cp/mL, and an intra-laboratory SD of 0.03 to 0.20 log₁₀ cp/mL during the implementation phase, and an inter-laboratory SD of 0.19 log₁₀ cp/mL, and an intra-laboratory SD 0.07 to 0.18 log₁₀ cp/mL during the trial phase. Three EQA panels and three linearity panels showed similarly small variability during implementation as well as within the trial phase.

Conclusion

This data shows that TTV load measurement can be standardized for use in a multinational clinical trial. By using IQC, LP and EQA samples, the quality and integrity of the assay can be compared between laboratories and precise and accurate results can be generated.

背景：器官移植后的免疫抑制药物通常通过治疗药物监测来确定剂量。然而，抗排斥药物的低浓度水平并不能充分预测排斥或感染。TTVguideIT 试验是一项多国临床试验，旨在评估通过 qPCR 评估托克替诺病毒（TTV）载量的安全性，以替代谷值水平的他克莫司剂量：方法：在临床试验之前和期间，通过分析参与试验的 13 家临床病毒学实验室使用各自的标准检测平台进行的内部质量控制 (IQC)、外部质量评估 (EQA) 和线性分析，评估了 TTV R-GENE® 检测方法在实验室内部和实验室之间的变异性、准确性和精密度：参与实验室在实施阶段检测了 130 次目标值为 4 log10 copies/mL (cp/mL) 的 IQC 样品，在试验阶段检测了 987 次。在实施阶段，实验室间标准偏差（SD）为 0.17 log10 cp/mL，实验室内标准偏差为 0.03 至 0.20 log10 cp/mL；在试验阶段，实验室间标准偏差为 0.19 log10 cp/mL，实验室内标准偏差为 0.07 至 0.18 log10 cp/mL。三个 EQA 面板和三个线性度面板在实施期间和试验阶段也显示出类似的小变异性：这些数据表明，TTV 负荷测量可标准化用于跨国临床试验。通过使用 IQC、LP 和 EQA 样品，可以在不同实验室之间比较检测的质量和完整性，并得出精确和准确的结果。

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引用次数: 0