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Optimization of pan-lyssavirus LN34 assay for streamlined rabies diagnostics by real-time RT-PCR 通过实时 RT-PCR 优化用于简化狂犬病诊断的泛赖病毒 LN34 检测方法。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-21 DOI: 10.1016/j.jviromet.2024.115070
Crystal M. Gigante , Vaughn Wicker , Kimberly Wilkins , Melanie Seiders , Hui Zhao , Puja Patel , Lillian Orciari , Rene Edgar Condori , Lisa Dettinger , Pamela Yager , Dongxiang Xia , Yu Li
Reliable, validated diagnostic tests are critical for rabies control in animals and prevention in people. We present a performance assessment and updates to the LN34 real-time RT-PCR assay for rabies diagnosis in postmortem animal brain samples. In two U.S. laboratories during 2017–2022, routine used of the LN34 assay produced excellent diagnostic sensitivity (99.72–100 %) and specificity (99.99–100 %) compared to the direct fluorescence antibody test (DFA). Almost all (>90 %) DFA indeterminate results caused by non-specific or atypical fluorescence were negative by LN34 testing, representing up to 111 cases where unnecessary post-exposure prophylaxis could be avoided. LN34 assay original primer sequences showed low sensitivity for some rare lyssaviruses. Increased primer concentration combined with new primer formulation showed improved performance for impacted lyssaviruses with no loss in performance across diverse rabies virus variants from clinical samples. The updated LN34 and internal control assays were combined into a single-well LN34 multiplexed (LN34M) format, run at half reagent volumes. The LN34M assay showed similar detection of rabies virus to the singleplexed assay with simplified assay set-up, lower cost, and improved quality controls.
可靠、有效的诊断测试对于动物狂犬病控制和人类狂犬病预防至关重要。我们介绍了用于动物死后脑样本狂犬病诊断的 LN34 实时 RT-PCR 检测的性能评估和更新。2017年至2022年期间,在美国的两个实验室中,与直接荧光抗体检测法(DFA)相比,LN34检测法的常规使用产生了极佳的诊断灵敏度(99.72%至100%)和特异性(99.99%至100%)。几乎所有(大于 90%)由非特异性或非典型性荧光引起的 DFA 不确定结果都在 LN34 检测中呈阴性,这代表多达 111 个病例可以避免不必要的暴露后预防。LN34 检测法的原始引物序列对一些罕见的拉伊沙病毒灵敏度较低。提高引物浓度并采用新的引物配方后,对受影响的百日咳病毒的灵敏度有所提高,而对来自临床样本的各种狂犬病病毒变种的灵敏度却没有降低。更新后的 LN34 和内部对照测定合并为单孔 LN34 多路复用(LN34M)格式,以一半试剂量运行。LN34M 检测法的狂犬病病毒检测结果与单孔复用检测法相似,但简化了检测设置、降低了成本并改进了质量控制。
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引用次数: 0
Accurate vector copy number determination in gammaretroviral vector producer cell clones using triplex digital droplet PCR 利用三重数字液滴聚合酶链式反应准确测定伽马逆转录病毒载体生产细胞克隆中的载体拷贝数。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-19 DOI: 10.1016/j.jviromet.2024.115075
Tomomine Iida , Yoshiki Nakamura , Katsuhiko Yamamoto , Eiki Maeda , Yukihiro Ikeda
Gammaretroviral vectors are widely used in cellular and gene therapy products because of the availability of stable vector producer cells. Accurately assessing vector copy number (VCN) is critical for selecting appropriate clones to avoid the risks of homologous recombination and complications in mutation detection. Traditional methods such as quantitative polymerase chain reaction (PCR) and Southern blotting have limitations in accuracy and throughput. This study presents a triplex droplet digital PCR (ddPCR) method for analyzing the VCN in gammaretroviral vector producer cells. We designed a universal primer– probe set targeting the packaging signal sequence common to murine leukemia virus– and murine stem cell virus– based gammaretroviral vectors. Two reference genes were selected after karyotyping the PG13 gammaretroviral vector packaging cell line to identify stable chromosomes. The triplex ddPCR assay was optimized and verified using PG13 cells transduced with constructs of different transgene and vector backbones. The assay showed high concordance with Southern blot. Using multiple reference genes ensures accurate and robust VCN assessment, especially in cell lines with chromosomal instability. This method improves the clone selection process for gammaretroviral vector producer cells, accelerates the development of novel cellular and gene therapy products, and ensures their rapid delivery to patients.
由于可以获得稳定的载体生产细胞,伽马逆转录病毒载体被广泛应用于细胞和基因治疗产品中。准确评估载体拷贝数(VCN)对于选择合适的克隆以避免同源重组风险和突变检测的复杂性至关重要。定量聚合酶链反应(PCR)和 Southern 印迹等传统方法在准确性和通量方面存在局限性。本研究提出了一种三重液滴数字 PCR(ddPCR)方法,用于分析伽马逆转录病毒载体生产细胞中的 VCN。我们设计了一套通用引物-探针,以鼠白血病病毒和鼠干细胞病毒为基础的伽马逆转录病毒载体所共有的包装信号序列为目标。在对 PG13 伽玛逆转录病毒载体包装细胞系进行核型鉴定以确定稳定的染色体后,我们选择了两个参考基因。使用不同转基因和载体骨架构建体转导的 PG13 细胞对三重 ddPCR 检测进行了优化和验证。该检测方法与 Southern 印迹的一致性很高。使用多个参考基因可确保准确、稳健地评估 VCN,尤其是在染色体不稳定的细胞系中。这种方法改进了伽马逆转录病毒载体生产细胞的克隆选择过程,加快了新型细胞和基因治疗产品的开发,并确保它们能迅速送达患者手中。
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引用次数: 0
Evaluation of the Alinity m CMV assay for detecting and quantifying cytomegalovirus DNA in non-plasma samples 评估用于检测和量化非血浆样本中巨细胞病毒 DNA 的 Alinity m CMV 检测法。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-19 DOI: 10.1016/j.jviromet.2024.115069
Anaïs Scohy , Maria A. Argudín , Florence Kabera , Nathalie Olive , Benoît Kabamba Mukadi
CMV infection remains a well-recognized threat in immunocompromised patients and is a major cause of congenital infection. If plasma and whole blood are routinely used as clinical samples for detection of CMV infection and disease, CMV laboratory testing in non-blood samples is becoming more and more relevant to support the diagnosis, prognosis and management of CMV infection. Accurate CMV viral load assessment in various body fluids is therefore essential. We evaluated the performance of the Alinity m CMV assay for detecting and quantifying CMV in plasma, amniotic fluid, bronchoalveolar lavage, cerebrospinal fluid, saliva and urine. Using a commercially available CMV reference panel and CMV culture supernatant, we assessed the linearity and accuracy of the Alinity m CMV assay across the different sample types. Excellent linear correlations (r values > 0.98) and a good accuracy (bias < ± 0.50 Log10 IU/mL and SD < 0.23) were observed. In conclusion, the Alinity m CMV assay is suitable to detect and quantify CMV DNA in plasma but also in all non-plasma samples tested. Random and continuous access capabilities of the Alinity m enable rapid and efficient laboratory detection and quantification of CMV DNA.
CMV 感染在免疫力低下的患者中仍是一个公认的威胁,也是先天性感染的一个主要原因。如果说血浆和全血是检测 CMV 感染和疾病的常规临床样本,那么非血液样本中的 CMV 实验室检测对于支持 CMV 感染的诊断、预后和管理则变得越来越重要。因此,准确评估各种体液中的 CMV 病毒载量至关重要。我们评估了 Alinity m CMV 检测试剂盒检测和定量血浆、羊水、支气管肺泡灌洗液、脑脊液、唾液和尿液中 CMV 的性能。我们使用市售的 CMV 参考面板和 CMV 培养上清,评估了 Alinity m CMV 检测法在不同样本类型中的线性和准确性。我们观察到了极好的线性相关性(r 值 > 0.98)和良好的准确性(偏差 < ± 0.50 Log10 IU/mL,SD < 0.23)。总之,Alinity m CMV 检测试剂盒不仅适用于检测血浆中的 CMV DNA,也适用于检测所有非血浆样本中的 CMV DNA。Alinity m 的随机和连续访问功能可实现快速、高效的 CMV DNA 实验室检测和定量。
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引用次数: 0
Development of polyclonal chicken egg yolk immunoglobulin Y (IgY) antibodies targeting SARS-CoV-2 multi-epitope antigen 针对 SARS-CoV-2 多表位抗原的多克隆鸡卵黄免疫球蛋白 Y (IgY) 抗体的开发。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-17 DOI: 10.1016/j.jviromet.2024.115062
Azzania Fibriani, Katerina Naisanu, Nicholas Yamahoki, Denti Rizki Kinanti
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is the primary cause of the Coronavirus disease 2019 (COVID-19) pandemic, which affects millions of people worldwide with high levels of infectivity and mortality. However, the antibodies developed for COVID-19 research and diagnostics are still limited. Therefore, in this study, we developed polyclonal immunoglobulin (IgY) antibodies from chicken egg yolk targeting multi-epitope antigen of SARS-CoV-2. After immunizing hens with a SARS-CoV-2 multi-epitope peptide, IgY antibodies were isolated from chicken eggs and further characterized using SDS-PAGE and ELISA. The results showed that the IgY antibodies were successfully isolated from egg yolks. The sandwich ELISA results demonstrated that the isolated IgYs could bind to SARS-CoV-2 antigens, both the multi-epitope peptide and the trimeric Spike. Furthermore, the developed polyclonal antibodies could recognize SARS-CoV-2 in human nasopharyngeal swab samples, even at the lowest concentration (dilution at 1:10000). Thus, it can be concluded that the developed polyclonal IgYs were successfully produced and have the potential to be applied in the development of COVID-19 diagnostics.
严重急性呼吸系统综合征-冠状病毒-2(SARS-CoV-2)是冠状病毒病 2019(COVID-19)大流行的主要原因,它影响着全球数百万人,感染率和死亡率都很高。然而,为 COVID-19 研究和诊断开发的抗体仍然有限。因此,在本研究中,我们从鸡卵黄中开发了针对 SARS-CoV-2 多表位抗原的多克隆免疫球蛋白(IgY)抗体。用 SARS-CoV-2 多表位肽免疫母鸡后,我们从鸡卵中分离出了 IgY 抗体,并用 SDS-PAGE 和 ELISA 对其进行了进一步鉴定。结果显示,从蛋黄中成功分离出了 IgY 抗体。夹心酶联免疫吸附试验结果表明,分离出的 IgYs 能与 SARS-CoV-2 抗原结合,包括多表位肽和三聚 Spike。此外,即使在最低浓度(1:10000 稀释度)下,所开发的多克隆抗体也能识别人类鼻咽拭子样本中的 SARS-CoV-2。因此,可以得出结论,研制成功的多克隆 IgYs 有潜力应用于 COVID-19 诊断方法的开发。
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引用次数: 0
Optimisation of a multiplexed, high throughput assay to measure neutralising antibodies against SARS-CoV-2 variants 优化多路复用高通量测定法,以测定针对 SARS-CoV-2 变体的中和抗体。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-16 DOI: 10.1016/j.jviromet.2024.115073
Caroline L. Ashley , Malik Bloul , Sibel Alca , Lachlan Smith , Wang Jin , David Khoury , Claudio Counoupas , Miles Davenport , James A. Triccas , Megan Steain
A multiplexed, lentivirus-based pseudovirus neutralisation assay (pVNT) was developed for high-throughput measurement of neutralising antibodies (nAbs) against three distinct SARS-CoV-2 spike variants. Intra-assay variability was minimised by optimising the plate layout and determining an optimal percentage transduction for the pseudovirus inoculum. Comparison of EC50 titres between single and multiplexed pVNT assays showed no significant differences, indicating reliability of the multiplexed assay. Evaluation of convalescent human sera confirmed assay robustness, with consistent EC50 titres for variant pseudoviruses relative to the ancestral strain observed across single and multiplexed assays. This multiplexed pVNT provides a reliable tool for assessing nAb responses against SARS-CoV-2 variants and could be used to accelerate preclinical vaccine assessment in preparation for the next coronavirus pandemic.
开发了一种基于慢病毒的多重伪病毒中和试验(pVNT),用于高通量测定针对三种不同的 SARS-CoV-2 尖峰变体的中和抗体(nAbs)。通过优化平板布局和确定伪病毒接种体的最佳转导百分比,最大限度地减少了测定内变异性。比较单一和多重 pVNT 检测的 EC50 滴度没有发现明显差异,这表明多重检测是可靠的。对康复期人类血清的评估证实了测定的稳健性,在单一和多重测定中观察到的变异伪病毒相对于祖先毒株的 EC50 滴度是一致的。这种多重 pVNT 为评估针对 SARS-CoV-2 变异株的 nAb 反应提供了可靠的工具,可用于加快临床前疫苗评估,为下一次冠状病毒大流行做准备。
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引用次数: 0
Evaluation and comparison of three high throughput assays (Alinity m CMV, Aptima CMV Quant and cobas CMV) for quantifying CMV DNA in plasma samples 评估和比较用于定量血浆样本中 CMV DNA 的三种高通量检测方法(Alinity m CMV、Aptima CMV Quant 和 cobas CMV)。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-15 DOI: 10.1016/j.jviromet.2024.115068
Jodie D’Costa, Doris Chibo, Katherine Soloczynskyj, Mitchell Batty, Rizmina Sameer, Elaine Lee, Thomas Tran, Dimi Mavroulis, Megan Gooey, Eloise Williams, Kathy Jackson

Background

Cytomegalovirus (CMV) can cause symptomatic CMV syndrome or tissue-invasive CMV disease in immunocompromised individuals, including solid-organ transplant and hematopoietic stem cell transplant recipients. In these populations, monitoring of CMV load is essential, assessing both risk of disease and response to antiviral therapy. High throughput commercial assays are currently available for CMV quantitation, but they are often evaluated independently, with few studies comparing these assays. This study evaluated CMV quantitative assays for use with the Roche cobas 6800, Abbott Alinity m and Hologic Panther platforms using stored patient plasma.

Methods

Analytical evaluation was performed using the 1st WHO international standard for human CMV for Nucleic Acid Amplification Techniques (cobas and Alinity m) or the Hologic CMV QC Calibrator 6 (Aptima). Parallel testing of 136 clinical plasma samples was performed across the three platforms.

Results

Linearity for each assay ranged from 98.6 % to 99.96 % and precision and limit of quantitation were as expected with little variation between platforms. 136 clinical plasma samples were evaluated with similar agreement observed between each assay. The greatest positive agreement was between the Aptima Quant and Alinity m assays (95.6 %, 95 % CI 89–98.6 %) and the lowest between the Aptima Quant and cobas assays (94.1 %, 87.4–97.5 %).

Conclusions

All assays were sensitive and accurate when quantifying CMV, and performance across all 3 assays was comparable for monitoring CMV viral loads in patient plasma.
背景:巨细胞病毒(CMV)可导致免疫功能低下者(包括实体器官移植和造血干细胞移植受者)出现无症状的 CMV 综合征或组织侵袭性 CMV 疾病。在这些人群中,监测 CMV 病毒载量至关重要,可评估疾病风险和对抗病毒治疗的反应。目前已有用于 CMV 定量的高通量商业检测方法,但这些检测方法通常是独立评估的,很少有研究对这些检测方法进行比较。本研究使用储存的患者血浆对罗氏 cobas 6800、雅培 Alinity m 和 Hologic Panther 平台的 CMV 定量检测进行了评估:使用核酸扩增技术(cobas 和 Alinity m)或 Hologic CMV QC Calibrator 6 (Aptima)进行分析评估。三个平台同时检测了 136 份临床血浆样本:结果:每种检测方法的线性范围在 98.6% 到 99.96% 之间,精密度和定量限符合预期,不同平台之间的差异很小。对 136 份临床血浆样本进行了评估,发现每种检测方法之间的一致性相似。Aptima Quant 和 Alinity m 检测法之间的正相关性最高(95.6%,95% CI 89-98.6%),Aptima Quant 和 cobas 检测法之间的正相关性最低(94.1%,87.4-97.5%):结论:在定量检测 CMV 时,所有检测方法的灵敏度和准确度都很高,所有 3 种检测方法在监测患者血浆中 CMV 病毒载量方面的性能相当。
{"title":"Evaluation and comparison of three high throughput assays (Alinity m CMV, Aptima CMV Quant and cobas CMV) for quantifying CMV DNA in plasma samples","authors":"Jodie D’Costa,&nbsp;Doris Chibo,&nbsp;Katherine Soloczynskyj,&nbsp;Mitchell Batty,&nbsp;Rizmina Sameer,&nbsp;Elaine Lee,&nbsp;Thomas Tran,&nbsp;Dimi Mavroulis,&nbsp;Megan Gooey,&nbsp;Eloise Williams,&nbsp;Kathy Jackson","doi":"10.1016/j.jviromet.2024.115068","DOIUrl":"10.1016/j.jviromet.2024.115068","url":null,"abstract":"<div><h3>Background</h3><div>Cytomegalovirus (CMV) can cause symptomatic CMV syndrome or tissue-invasive CMV disease in immunocompromised individuals, including solid-organ transplant and hematopoietic stem cell transplant recipients. In these populations, monitoring of CMV load is essential, assessing both risk of disease and response to antiviral therapy. High throughput commercial assays are currently available for CMV quantitation, but they are often evaluated independently, with few studies comparing these assays. This study evaluated CMV quantitative assays for use with the Roche cobas 6800, Abbott Alinity m and Hologic Panther platforms using stored patient plasma.</div></div><div><h3>Methods</h3><div>Analytical evaluation was performed using the 1st WHO international standard for human CMV for Nucleic Acid Amplification Techniques (cobas and Alinity m) or the Hologic CMV QC Calibrator 6 (Aptima). Parallel testing of 136 clinical plasma samples was performed across the three platforms.</div></div><div><h3>Results</h3><div>Linearity for each assay ranged from 98.6 % to 99.96 % and precision and limit of quantitation were as expected with little variation between platforms. 136 clinical plasma samples were evaluated with similar agreement observed between each assay. The greatest positive agreement was between the Aptima Quant and Alinity m assays (95.6 %, 95 % CI 89–98.6 %) and the lowest between the Aptima Quant and cobas assays (94.1 %, 87.4–97.5 %).</div></div><div><h3>Conclusions</h3><div>All assays were sensitive and accurate when quantifying CMV, and performance across all 3 assays was comparable for monitoring CMV viral loads in patient plasma.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115068"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Quantitative and qualitative analysis of seroconversion after one year of vaccination with inactivated SARS-CoV-2 vaccine (CoronaVac®) in healthcare workers: Cross-sectional analytical study "医护人员接种 SARS-CoV-2 灭活疫苗 (CoronaVac®) 一年后血清转换的定量和定性分析:横断面分析研究"。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-15 DOI: 10.1016/j.jviromet.2024.115067
Júlia Gomes da Silva , Viviana Galimberti Arruk , Glaucia Raquel Luciano da Veiga , Luiz Vinícius de Alcantara Sousa , Beatriz da Costa Aguiar Alves , Fernando Luiz Affonso Fonseca , Inneke Marie van der Heijden Natário
A descriptive study was carried out with health professionals in Sao Paulo city. Were included individuals vaccinated with 2 doses of the inactivated vaccine. Demographic, clinical and vaccination information was obtained from professionals with or without comorbidities. Two serological assays were used to identify the presence and quantity of anti-Spike IgG in serum samples. 433 healthy healthcare professionals were included and 58.9 % completed the 4 clinical stages of serological assessment. Among adults and elderly people, 25.2 % had chronic diseases (hypertension 50.5 %, diabetes 10 % and obesity 6.5 %). Most individuals have 95 % protection in the first 3 months after the second dose, and 67.68 % protection after 6 months. Total antibodies ranged from 3 to 10 on the reactivity index, and the anti-RBD IgG levels were high. CoronaVac has a 94 % seroconversion rate after 2 doses and can prevent serious cases and outbreaks of the disease, if used on a large scale.
我们对圣保罗市的医疗专业人员进行了一项描述性研究。研究对象包括接种过两剂灭活疫苗的人员。研究人员从患有或不患有合并症的专业人员那里获得了人口统计学、临床和疫苗接种信息。采用了两种血清学检测方法来确定血清样本中是否存在抗斯派克 IgG 及其数量。共纳入了 433 名健康的医疗保健专业人员,其中 58.9% 完成了血清学评估的 4 个临床阶段。在成年人和老年人中,25.2%患有慢性疾病(高血压50.5%、糖尿病10%和肥胖6.5%)。大多数人在注射第二针后的头 3 个月内有 95% 的保护率,6 个月后有 67.68% 的保护率。总抗体的反应指数从3到10不等,抗RBD IgG水平较高。CoronaVac两剂后的血清转换率为94%,如果大规模使用,可以预防严重病例和疾病爆发。
{"title":"Quantitative and qualitative analysis of seroconversion after one year of vaccination with inactivated SARS-CoV-2 vaccine (CoronaVac®) in healthcare workers: Cross-sectional analytical study","authors":"Júlia Gomes da Silva ,&nbsp;Viviana Galimberti Arruk ,&nbsp;Glaucia Raquel Luciano da Veiga ,&nbsp;Luiz Vinícius de Alcantara Sousa ,&nbsp;Beatriz da Costa Aguiar Alves ,&nbsp;Fernando Luiz Affonso Fonseca ,&nbsp;Inneke Marie van der Heijden Natário","doi":"10.1016/j.jviromet.2024.115067","DOIUrl":"10.1016/j.jviromet.2024.115067","url":null,"abstract":"<div><div>A descriptive study was carried out with health professionals in Sao Paulo city. Were included individuals vaccinated with 2 doses of the inactivated vaccine. Demographic, clinical and vaccination information was obtained from professionals with or without comorbidities. Two serological assays were used to identify the presence and quantity of anti-Spike IgG in serum samples. 433 healthy healthcare professionals were included and 58.9 % completed the 4 clinical stages of serological assessment. Among adults and elderly people, 25.2 % had chronic diseases (hypertension 50.5 %, diabetes 10 % and obesity 6.5 %). Most individuals have 95 % protection in the first 3 months after the second dose, and 67.68 % protection after 6 months. Total antibodies ranged from 3 to 10 on the reactivity index, and the anti-RBD IgG levels were high. CoronaVac has a 94 % seroconversion rate after 2 doses and can prevent serious cases and outbreaks of the disease, if used on a large scale.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115067"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells 绘制受感染植物细胞中病毒颗粒和多聚体内马铃薯病毒 A RNA 基因组的图谱并对其进行定量。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-15 DOI: 10.1016/j.jviromet.2024.115066
Pinky Dutta, Kristiina Mäkinen
Potato virus A belongs to the genus Potyvirus, a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, viz., translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.
马铃薯病毒 A 属于马铃薯病毒属(Potyvirus),是一组感染全球农作物的单链正感 RNA 病毒。为了启动对宿主的感染,其基因组在感染周期中会参与不同的活动,即翻译、复制和封装。为了仔细研究壶状病毒感染周期的各个阶段并破译其致病策略,已经开展了广泛的研究。然而,在特定时间点参与翻译和病毒形成的病毒 RNA 数量却不详。在这项研究中,我们量化了感染植物组织中以病毒形式存在的病毒 RNA 和与宿主多聚体结合的病毒 RNA 占病毒 RNA 总量的百分比。我们采用免疫捕获反转录 PCR 和多聚体分析的修订版来解决我们的疑问。我们测试了三种不同的包被抗体浓度,并进一步优化了免疫捕获反转录 PCR 方案,以解决其在结合和保留病毒颗粒方面的局限性。我们的结果表明,大部分病毒 RNA(69%)以包被基因组的形式存在,而病毒 RNA 总量的 3% 与宿主多聚体结合。这些发现对于正确解释定量转化研究至关重要,因为在定量转化研究中,必须将多聚体相关转录本的数量与合成的蛋白质数量联系起来。
{"title":"Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells","authors":"Pinky Dutta,&nbsp;Kristiina Mäkinen","doi":"10.1016/j.jviromet.2024.115066","DOIUrl":"10.1016/j.jviromet.2024.115066","url":null,"abstract":"<div><div>Potato virus A belongs to the genus <em>Potyvirus,</em> a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, <em>viz.</em>, translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115066"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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
Wastewater sample storage for physicochemical and microbiological analysis 用于理化和微生物分析的废水样本存储。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-14 DOI: 10.1016/j.jviromet.2024.115063
Gordon Webster , Shrinivas Nivrutti Dighe , William B. Perry , Ewan H. Stenhouse , Davey L. Jones , Peter Kille , Andrew J. Weightman
Wastewater-based epidemiology (WBE) is a crucial tool for health and environmental monitoring, providing real-time data on public health indicators by analysis of sewage samples. Ensuring the integrity of these samples from collection to analysis is paramount. This study investigates the effects of different cold-storage conditions on the integrity of wastewater samples, focusing on both microbiological markers (such as extractable nucleic acids, SARS-CoV-2, and crAssphage) and physicochemical parameters (including ammonium, orthophosphate, pH, conductivity, and turbidity). Composite samples from the raw wastewater influent from five wastewater treatment works in South Wales, UK, were stored at 4°C, -20°C, and -80°C, and subjected to up to six freeze-thaw cycles over one year. The study found significant effects of storage temperature on the preservation of certain WBE markers, with the best yield most frequently seen in samples stored at -80°C. However, the majority of WBE markers showed no significant difference between storage at -80°C or at 4°C, demonstrating that it may not always be necessary to archive wastewater samples at ultra-low temperatures, thus reducing CO2 emissions and laboratory energy costs. These findings underscore the importance of optimized storage conditions to maintain sample integrity, while ensuring accurate and reliable WBE data for public health and environmental monitoring.
污水流行病学(WBE)是健康和环境监测的重要工具,通过分析污水样本提供有关公共健康指标的实时数据。确保这些样本从采集到分析的完整性至关重要。本研究调查了不同冷藏条件对废水样本完整性的影响,重点关注微生物标记物(如可提取核酸、SARS-CoV-2 和 crAssphage)和理化参数(包括氨、正磷酸盐、pH 值、电导率和浊度)。研究人员将英国南威尔士五个污水处理厂的原废水进水复合样本分别储存在 4°C、-20°C 和 -80°C,并在一年内进行了多达六次冻融循环。研究发现,储存温度对某些水生生物碱标记物的保存有明显影响,在-80°C下储存的样本产量最高。不过,大多数水生生物标记物在-80°C 和 4°C 下的保存效果并无明显差异,这表明并不总是有必要在超低温下保存废水样本,从而减少二氧化碳排放和实验室能源成本。这些发现强调了优化存储条件对保持样本完整性的重要性,同时确保为公共卫生和环境监测提供准确可靠的水生生物数据。
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引用次数: 0
Evaluation of the impact of hollow fiber pore size and membrane material on virus concentration using a handheld hollow fiber method 使用手持式中空纤维法评估中空纤维孔径和膜材料对病毒浓度的影响。
IF 2.2 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-14 DOI: 10.1016/j.jviromet.2024.115065
Shinsuke Higuchi , Tatsuki Satou , Yuki Uchida
Virus concentration using hollow fibers is widely used for vaccine production to maintain viral infectivity with low shear stress and to allow for easier scale-up of production. However, research laboratories often have limited available viral materials at the early stage of vaccine development, making it difficult to find an optimal hollow-fiber. In addition, few research articles have reported on optimizing hollow fiber pore size and membrane structure for virus concentration. In this study, the previously established handheld hollow fiber virus concentration method was modified to reduce the sample volume required and to enable simple and easy hollow fiber screening. The handheld hollow fiber screening method for virus concentration was confirmed to be effective using Zika as a model virus.
使用中空纤维浓缩病毒被广泛用于疫苗生产,以在低剪切应力下保持病毒的感染性,并使生产规模更容易扩大。然而,在疫苗开发的早期阶段,研究实验室可用的病毒材料往往有限,因此很难找到最佳的中空纤维。此外,关于优化中空纤维孔径和膜结构以提高病毒浓度的研究文章也寥寥无几。本研究对之前建立的手持式中空纤维病毒浓缩方法进行了改进,以减少所需的样品量,并实现简单易行的中空纤维筛选。以寨卡病毒为模型,证实了手持式中空纤维病毒浓缩筛选方法的有效性。
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引用次数: 0
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Journal of virological methods
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