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Potential of recombinant avian adeno-associated virus as a viral vector for CRISPR/Cas9 delivery to avian cells 重组禽腺相关病毒作为CRISPR/Cas9载体的潜力
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-09 DOI: 10.1016/j.jviromet.2025.115263
Takumi Terada , Sodai Fujii , Nanako Yamanishi , Ryota Kajihara , Tenkai Watanabe , Ryo Ezaki , Hiroyuki Horiuchi , Mei Matsuzaki
While genome editing has been established in chickens, where cultured primordial germ cell (PGC) systems are available, the implementation of genome editing remains a major challenge in many other birds due to the lack of robust PGC culture methods. Therefore, the development of reliable and efficient tools can significantly accelerate precision genome modification in avian species. Here, we evaluated the applicability of recombinant avian adeno-associated virus (rA3V) as a delivery vector for a CRISPR/Cas9 construct in avian cells using Staphylococcus aureus-derived Cas9 (SaCas9) and single-guide RNA (sgRNA). Infection with rA3V particles carrying an EGFP expression cassette (rA3V-EGFP) successfully induced EGFP expression in chicken fibroblasts (DF-1) cells, with approximately 80 % EGFP-positive cells at the maximum multiplicity of infection (MOI = 10,000). In plasmid-based transfection experiments, sgRNAs targeting the chicken tyrosinase locus and SaCas9 exhibited DNA cleavage activity in DF-1 cells. Furthermore, infection with rA3V particles encoding these CRISPR components successfully introduced indel mutations into the tyrosinase gene in DF-1 cells, with a calculated indel frequency of approximately 5.4 % at MOI = 40,000 without drug selection. Although EGFP expression was observed in quail fibrosarcoma cells, the percentage of EGFP-positive cells was much lower than that in DF-1 cells. In addition, in vivo infection with rA3V-EGFP of the chicken blastoderm failed to induce EGFP expression in germline cells, even at the highest applicable viral dose. In summary, rA3V can be used as a genome-editing vector in birds, although further investigation of its infectivity and tropism is necessary to expand its applicability to diverse avian species.
虽然基因组编辑已经在鸡中建立,其中培养的原始生殖细胞(PGC)系统是可用的,但由于缺乏强大的PGC培养方法,在许多其他鸟类中实施基因组编辑仍然是一个主要挑战。因此,开发可靠、高效的工具可以显著加快鸟类基因组的精确修饰。在这里,我们利用金黄色葡萄球菌衍生的Cas9 (SaCas9)和单导RNA (sgRNA)评估了重组禽腺相关病毒(rA3V)作为CRISPR/Cas9构建物在禽细胞中的传递载体的适用性。携带EGFP表达盒的rA3V颗粒(rA3V-EGFP)感染鸡成纤维细胞(DF-1)成功诱导EGFP表达,在最大感染倍数(MOI = 10,000)时,EGFP阳性细胞约占80%。在质粒转染实验中,靶向鸡酪氨酸酶位点和SaCas9的sgRNAs在DF-1细胞中表现出DNA切割活性。此外,编码这些CRISPR成分的rA3V颗粒感染成功地将indel突变引入DF-1细胞的酪氨酸酶基因中,在MOI为40000时计算出的indel频率约为5.4%,没有药物选择。虽然在鹌鹑纤维肉瘤细胞中观察到EGFP的表达,但EGFP阳性的细胞比例远低于DF-1细胞。此外,即使在最高适用病毒剂量下,rA3V-EGFP在鸡胚皮体内感染也不能诱导种系细胞表达EGFP。综上所述,rA3V可以作为鸟类基因组编辑载体,但需要进一步研究其感染性和嗜性,以扩大其在不同鸟类物种中的适用性。
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引用次数: 0
Curcumin inhibits HIV-1 by modulating FOXP3 and suppressing CCR5 via PI3K/AKT and JAK/STAT pathways 姜黄素通过PI3K/AKT和JAK/STAT通路调节FOXP3和抑制CCR5抑制HIV-1
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-06 DOI: 10.1016/j.jviromet.2025.115261
Mengyuan Shi , Qing Li , Wenjin Zheng , Qingya Li , Min Jiang , Jingyi Zhang , Zhe Wang , Lu Qiao , Long Feng
Despite advances in antiretroviral therapy, HIV-1 persistence and immune dysregulation remain unresolved challenges. Here, we demonstrate that curcumin, a low-toxicity natural compound, can inhibit HIV-1 through simultaneous inhibition of the PI3K/AKT and JAK/STAT pathways, leading to downregulation of the viral co-receptor CCR5 and the immune checkpoint transcription factor FOXP3. Using CHIP and EMSA experiments, we found that curcumin disrupts the binding of FOXP3 to the CCR5 promoter, thereby reducing viral entry. Network pharmacology and molecular docking identified STAT3 and AKT1 as key targets. Most importantly, we found that crosstalk between the PI3K/AKT and JAK/STAT pathways is a pharmacological axis for HIV-1 treatment through high-throughput sequencing technology, mass spectrometry and CO-IP experiments. Our findings provide a mechanistic basis for the repurposing of curcumin as an adjuvant to HAART, with implications for therapies targeting viral reservoirs.
尽管抗逆转录病毒治疗取得了进展,但HIV-1的持久性和免疫失调仍然是未解决的挑战。本研究表明,姜黄素是一种低毒天然化合物,可通过同时抑制PI3K/AKT和JAK/STAT通路抑制HIV-1,导致病毒共受体CCR5和免疫检查点转录因子FOXP3的下调。通过CHIP和EMSA实验,我们发现姜黄素破坏了FOXP3与CCR5启动子的结合,从而减少了病毒的进入。网络药理学和分子对接发现STAT3和AKT1是关键靶点。最重要的是,通过高通量测序技术、质谱分析和CO-IP实验,我们发现PI3K/AKT和JAK/STAT通路之间的串扰是HIV-1治疗的药理学轴。我们的研究结果为姜黄素作为HAART的辅助治疗提供了机制基础,对靶向病毒库的治疗具有指导意义。
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引用次数: 0
Performance evaluation of a SYBR Green-based real-time quantitative PCR for SARS-CoV-2 detection from animal oropharyngeal samples SYBR绿色实时荧光定量PCR检测动物口咽标本SARS-CoV-2的性能评价
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-05 DOI: 10.1016/j.jviromet.2025.115259
María Emilia Bravi , Nadia Analía Fuentealba , Natalia Brasso , Guillermo Hernan Sguazza , Marcelo Ricardo Pecoraro , Carlos Javier Panei
The global emergence of SARS-CoV-2 has highlighted the need for rapid, sensitive, and affordable diagnostic tools, not only for human health but also for animal surveillance within a One Health framework. This study aimed to evaluate the performance of a SYBR Green-based real-time quantitative PCR (qPCR) assay for the detection of SARS-CoV-2 from animal samples, focusing on domestic dogs and cats. A total of 140 oropharyngeal swab samples were collected and analyzed using primers targeting a 139-bp fragment of the N gene of SARS-CoV-2. The assay conditions were optimized through gradient PCR, primer concentration adjustment, and melting curve analysis. Cloning and quantification of the target gene allowed the determination of the limit of detection (LOD), which was estimated at 2.1 × 102 copies/µL. Among the samples tested, 13 were positive for SARS-CoV-2, confirmed by a commercial probe-based qPCR. The assay here evaluated demonstrated high specificity, with no cross-reactivity to canine or feline coronaviruses, and had a highly linear standard curve of 0.977 (R² = 0.997) with a value range of quantification cycle (Cq) from 9.25 to 34.89. In addition, it exhibited a 2-log increase in sensitivity compared to conventional PCR. The intra- and inter-assay coefficients of variation were below 1.1 % and 2 %, respectively, confirming high reproducibility. These results support the use of SYBR Green real-time qPCR as a cost-effective and reliable alternative for SARS-CoV-2 detection from animal samples, particularly in resource-limited settings, serving as a tool for epidemiological control of SARS-CoV-2 infection in animal populations.
SARS-CoV-2在全球的出现凸显了对快速、敏感和负担得起的诊断工具的需求,不仅是为了人类健康,也是为了在“同一个健康”框架内进行动物监测。本研究旨在评估基于SYBR green的实时定量PCR (qPCR)检测动物样本中SARS-CoV-2的性能,重点是家养狗和猫。收集140份口咽拭子样本,利用引物靶向SARS-CoV-2 N基因139 bp片段进行分析。通过梯度PCR、引物浓度调整、熔点曲线分析等方法优化检测条件。目的基因的克隆和定量确定了检测限(LOD),估计为2.1 × 102拷贝/µL。在检测的样本中,有13个样本呈SARS-CoV-2阳性,经基于探针的商业qPCR证实。该方法特异性高,对犬、猫冠状病毒无交叉反应,标准曲线线性度为0.977 (R²= 0.997),定量周期(Cq)取值范围为9.25 ~ 34.89。此外,与传统PCR相比,它的灵敏度增加了2倍。测定结果的组内变异系数小于1.1%,组间变异系数小于2%,重复性好。这些结果支持使用SYBR Green实时qPCR作为从动物样本中检测SARS-CoV-2的一种具有成本效益和可靠的替代方法,特别是在资源有限的环境中,可作为动物种群中SARS-CoV-2感染的流行病学控制工具。
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引用次数: 0
Evaluation of two IgG-scFv bispecific antibodies for neutralizing Omicron variants of SARS-CoV-2 两种IgG-scFv双特异性抗体中和SARS-CoV-2 Omicron变体的评价
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-05 DOI: 10.1016/j.jviromet.2025.115258
Diana Hinojosa-Trujillo , Freddy Dehesa-Canseco , Melissa García-Vega , Verónica Mata-Haro , Mario Solís-Hernández , Mónica Reséndiz-Sandoval , Fanglei Zuo , Harold Marcotte , Jesús Hernández
Bispecific antibodies (bsAbs) offer an alternative to monoclonal antibody (mAb) cocktails for addressing the loss of efficacy due to the rapid emergence of SARS-CoV-2 mutants. The structure and specificity of the parental antibodies influence the development of a highly neutralizing bsAb. To design an effective bsAb, the recognition of 44 single-chain fragment variable (scFv) antibodies against variants of SARS-CoV-2 was evaluated, along with an assessment of their ability to competitively bind to the receptor-binding domain (RBD) compared to the most potent neutralizing mAbs. From this analysis, three antibodies − 19n01, 01n21, and 01n27 − were identified for their broad recognition and non-competitive binding behavior. These antibodies were selected as the parental antibodies for the design of two bsAb. The bsAb bis L and bis H were engineered as IgG-scFv constructs, each with the secondary domain oriented differently to introduce new specificities. Both bsAbs retained the neutralizing capabilities of their parental antibodies in live-virus assays, neutralizing the Omicron variants BQ.1.1 and XBB.1.
双特异性抗体(bsAbs)是单克隆抗体(mAb)鸡尾酒的替代方案,可解决由于SARS-CoV-2突变体迅速出现而导致的疗效丧失问题。亲本抗体的结构和特异性影响高度中和性bsAb的发展。为了设计一种有效的bsAb,我们评估了44种针对SARS-CoV-2变体的单链片段变量(scFv)抗体的识别能力,并与最有效的中和单克隆抗体相比,评估了它们与受体结合结构域(RBD)的竞争性结合能力。从这个分析中,鉴定出三种抗体- 19n01, 01n21和01n27,它们具有广泛的识别和非竞争性结合行为。选择这些抗体作为亲本抗体设计两种bsAb。bsAb his L和his H被设计成IgG-scFv结构,每个结构域定向不同,以引入新的特异性。在活病毒试验中,两种bsab都保留了亲本抗体的中和能力,中和了Omicron变体BQ.1.1和XBB.1。
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引用次数: 0
A dual-target real-time PCR for proactive detection of Mpox variants 主动检测m痘变异的双目标实时PCR。
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-05 DOI: 10.1016/j.jviromet.2025.115260
Tracy D. Lee , Alan O’Dwyer , Michael Chan , Branco Cheung , Frankie Tsang , John R. Tyson , Kathleen L. Kolehmainen , Natalie A. Prystajecky , Agatha N. Jassem
In 2022, cases of Monkeypox virus (MPXV) in California contained a mutation in the TNF receptor gene (GR2G) that rendered the virus undetectable using a widely adopted public health diagnostic qPCR assay. This underscored the need for a dual-target PCR approach and prompted validation of a second target by the BCCDC Public Health Laboratory. In addition to the GR2G target validated in the original qPCR assay (and duplexed with the endogenous target human β-globin (HBG)), GP113 (OPG128) was identified and validated using both clinical samples and MPXV DNA controls. Mutations in GR2G and GP113 (found in the emerging clade Ib) were also addressed along with the updated target. The new triplex assay (GR2G/GP113/HBG) had 100 % inclusivity and 100 % accuracy with all clinical samples tested and did not cross-react with herpes simplex virus-1 or −2, varicella zoster virus, or enterovirus. It showed < 5 % coefficient of variance between replicates and had a limit-of-detection of 10 copies/μL for GR2G and GP113. The use of two targets presents redundancy against further mutations in MPXV and is recommended for use with all viral qPCR assays moving forward.
2022年,加利福尼亚州的猴痘病毒(MPXV)病例包含TNF受体基因(GR2G)突变,这使得使用广泛采用的公共卫生诊断qPCR检测无法检测到该病毒。这强调了双靶点PCR方法的必要性,并促使BCCDC公共卫生实验室对第二个靶点进行验证。除了在最初的qPCR实验中验证的GR2G靶点(并与内源性靶点人β-珠蛋白(HBG)双活)外,GP113 (OPG128)在临床样本和MPXV DNA对照中被鉴定和验证。GR2G和GP113的突变(在新兴分支Ib中发现)也与更新的靶标一起得到了解决。新的三重检测(GR2G/GP113/HBG)对所有临床样本检测具有100%的包容性和100%的准确性,并且不会与单纯疱疹病毒-1或-2、水痘带状疱疹病毒或肠病毒发生交叉反应。它显示
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引用次数: 0
Cryopreservation of chicken and duck tracheal rings and precision-cut lung slices: A promising tool for the rapid characterization of avian influenza viruses 鸡鸭气管环和精确切割肺片的低温保存:一种有前途的禽流感病毒快速表征工具
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-02 DOI: 10.1016/j.jviromet.2025.115257
Alessandra Napolitan , Elisa Mazzacan , Niccolò Fonti , Sofia Tomasoni , Erica Melchiotti , Claudia Zanardello , Lucrezia Vianello , Sami Ramzi , Valentina Panzarin , Marika Crimaudo , Ranieri Verin , Francesco Bonfante , Eva Mazzetto
Since its emergence in 1996, highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/96 lineage have diversified into multiple clades, culminating in the 2020–2021 global panzootic caused by H5N1 viruses of the clade 2.3.4.4b. Further reassortment events have significantly diversified the phenotypes of these viruses, underscoring the need for continuous monitoring and strain characterization to better adjust control measures and mitigate the impact of the disease in wild birds and poultry. Standardized, ready-to-use ex vivo tissue platforms for rapid phenotyping of avian influenza viruses (AIVs) offer a valid alternative to in vivo models that are financially, ethically and logistically demanding. We optimized explant production and cryopreservation protocols for chicken and duck tracheal organ cultures (cTOCs and dTOCs) and precision-cut lung slices (cPCLS and dPCLS), assessing post-thaw viability, histological integrity, and susceptibility to AIV infection. Trehalose supplementation of cryopreservation solutions based on dimethyl sulfoxide (DMSO) and fetal bovine serum (FBS) significantly improved tissue viability. Although cryopreserved tissues were less viable than the fresh explants, viral replication was similar and only a modest reduction in susceptibility to infection was observed. Finally, we used duck and chicken TOCs to assess the ability of cryopreserved explants to discriminate viruses based on their divergent fitness and host preference. These findings underscore the potential of cryopreserved TOCs and PCLS as additional tools for the phenotypic characterisation of emerging AIVs.
自1996年出现以来,A/Goose/Guangdong/1/96谱系的高致病性禽流感(HPAI)已分化成多个分支,最终在2020-2021年由2.3.4.4b分支的H5N1病毒引起的全球大流行中达到高潮。进一步的重配事件使这些病毒的表型显著多样化,强调需要持续监测和品系表征,以更好地调整控制措施并减轻该疾病对野生鸟类和家禽的影响。标准化的、即用型的离体组织平台可用于禽流感病毒(AIVs)的快速表型分析,为在体模型提供了一种有效的替代方案,而体内模型在经济、伦理和后勤方面都要求很高。我们优化了鸡和鸭气管器官培养(cTOCs和dTOCs)和精确切割肺切片(cPCLS和dPCLS)的外植体生产和冷冻保存方案,评估了解冻后的活力、组织学完整性和对AIV感染的易感性。以二甲亚砜(DMSO)和胎牛血清(FBS)为基础的冷冻保存液中添加海藻糖可显著提高组织活力。虽然冷冻保存的组织比新鲜外植体的存活率低,但病毒复制相似,对感染的易感性仅略有降低。最后,我们用鸭和鸡的TOCs来评估冷冻保存的外植体根据病毒的不同适应度和宿主偏好来区分病毒的能力。这些发现强调了冷冻保存的TOCs和PCLS作为新兴aiv表型表征的额外工具的潜力。
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引用次数: 0
Treeshrews as a potential reservoir: First detection of dengue virus serotype 2 in Malaysian treeshrew faeces 树鼩作为潜在宿主:首次在马来西亚树鼩粪便中检测到血清2型登革热病毒
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-08-31 DOI: 10.1016/j.jviromet.2025.115256
Zhen Yun Siew , Chen Zhe Tang , Siti Nor Asma Musa , Isaac Seow , Nur Alia Johari , Pooi Pooi Leong , Siew Tung Wong , Kenny Voon
Arboviruses are transmitted to humans and animals by arthropods and can be fatal. Dengue fever remains a major mosquito-borne disease in tropical regions, primarily spread by Aedes aegypti and Aedes albopictus. Despite vector control and vaccine efforts, dengue virus (DENV) continues to pose serious public health challenges in Malaysia. While non-human primates are known reservoirs in sylvatic cycles, the role of other mammals like treeshrews (Tupaia glis) is poorly understood. This study screened wild treeshrews in suburban Semenyih, Malaysia, for DENV and its serotype. From 2023–2024, fecal and urine samples were collected and pooled for molecular screening. Viral RNA was extracted and tested via RT-PCR targeting the Capsid-Premembrane (C-prM) region. Of 11 samples, three (27.3 %) were positive for DENV-2. Sequence analysis revealed the cosmopolitan genotype II, typically linked to human transmission, rather than sylvatic strains. Virus isolation in Vero and C6/36 cells showed cytopathic effects, though contamination hampered results. These findings suggest treeshrews may serve as incidental reservoirs or amplifying hosts of DENV-2, highlighting the need for wildlife surveillance to better understand dengue transmission and guide public health responses.
虫媒病毒通过节肢动物传播给人类和动物,可能是致命的。登革热仍然是热带地区一种主要的蚊媒疾病,主要由埃及伊蚊和白纹伊蚊传播。尽管在媒介控制和疫苗方面做出了努力,但登革热病毒(DENV)继续在马来西亚构成严重的公共卫生挑战。虽然非人类灵长类动物是已知的森林循环的储藏库,但其他哺乳动物如树鼩(图帕亚glis)的作用却知之甚少。本研究对马来西亚Semenyih郊区的野生树鼩进行了DENV及其血清型筛查。从2023年至2024年,收集粪便和尿液样本并汇总进行分子筛选。提取病毒RNA,并通过RT-PCR检测针对衣壳-膜前区(C-prM)。11份样本中,3份(27.3 %)DENV-2阳性。序列分析显示世界性基因型II,通常与人类传播有关,而不是森林菌株。病毒在Vero和C6/36细胞中的分离显示出细胞病变效应,尽管污染阻碍了结果。这些发现表明树鼩可能是DENV-2的附带宿主或扩增宿主,突出了野生动物监测的必要性,以便更好地了解登革热传播并指导公共卫生应对。
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引用次数: 0
Development and analytical validation of a quantitative PCR assay for the detection of Magellanic penguin herpesvirus 1 麦哲伦企鹅疱疹病毒1型定量PCR检测方法的建立及分析验证
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-08-28 DOI: 10.1016/j.jviromet.2025.115255
Maris J. Daleo , Laura A. Adamovicz , Karisa N. Tang , Matthew C. Allender
Herpesviruses are associated with disease in several aquatic bird species, including penguins. Magellanic penguin herpesvirus 1 (MagHV1) was initially detected in 58.3 % of oiled Magellanic penguins (Spheniscus magellanicus) in South America presenting with respiratory distress characterized by a combination of necrohemorrhagic tracheitis, fibrinous air sacculitis, pneumonia, and death. Additional exploration is needed to understand how herpesviruses affect penguin health; however, there is currently a lack of rapid, sensitive, and specific methods for detecting and quantifying herpesvirus infections in this taxon. To address this problem, we developed a real-time quantitative PCR (qPCR) assay for the detection of MagHV1 in penguins. Using a commercial program, TaqMan-MGB primer-probes targeting the DNA polymerase gene were designed in silico. Inter- and intra-assay variability, dynamic range, limit of detection, and analytical specificity were assessed to validate the assay per MIQE guidelines. The resulting assay was highly specific for MagHV1, failing to amplify fifteen closely related avian herpesviruses. It performed with high efficiency (slope =-3.336, R2 = 0.999, efficiency 99.40 %) and low inter- and intra-assay variability (coefficient of variation < 1.67 % at all dilutions). Reaction efficiency was not impacted by the presence of penguin DNA from known-negative tracheal swabs. This qPCR assay has a linear range of detection from 107 to 101 viral copies per reaction and provides a valuable tool in the surveillance and characterization of MagHV1 epidemiology in penguins. This assay can further be used to detect asymptomatic birds and as an effective tool to monitor infectious individuals.
疱疹病毒与包括企鹅在内的几种水禽的疾病有关。麦哲伦企鹅疱疹病毒1 (MagHV1)最初在南美洲58.3% %的油麦哲伦企鹅(Spheniscus magellanicus)中检测到,表现为呼吸窘迫,其特征是坏死性出血性气管炎、纤维性空气囊炎、肺炎和死亡。需要进一步的探索来了解疱疹病毒如何影响企鹅的健康;然而,目前缺乏快速、敏感和特异性的方法来检测和定量该分类群中的疱疹病毒感染。为了解决这一问题,我们建立了一种实时定量PCR (qPCR)方法来检测企鹅体内的MagHV1。利用商业程序,设计了针对DNA聚合酶基因的TaqMan-MGB引物探针。评估测定间和测定内的变异性、动态范围、检测限和分析特异性,以根据MIQE指南验证测定。结果对MagHV1具有高度特异性,不能扩增15种密切相关的禽疱疹病毒。该方法效率高(斜率=-3.336,R2 = 0.999,效率99.40 %),测定间和测定内变异性低(所有稀释度的变异系数<; 1.67 %)。反应效率不受已知阴性气管拭子中企鹅DNA存在的影响。该方法具有107 ~ 101个线性检测范围,为企鹅MagHV1流行病学监测和鉴定提供了有价值的工具。该试验可进一步用于检测无症状禽类,并作为监测感染个体的有效工具。
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引用次数: 0
Detection and characterization of neonatal cytomegalovirus through nanopore sequencing using flongle flow cells: Pilot study in Philadelphia, Pennsylvania 利用flongle流式细胞通过纳米孔测序检测和表征新生儿巨细胞病毒:在宾夕法尼亚州费城的初步研究
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-08-24 DOI: 10.1016/j.jviromet.2025.115245
Alvaro Proaño , Joe Chan , Gabrielle C. Galchen , Mian Umair Ahsan , Robert H. Gilman , Kenneth P. Smith , Kai Wang , Dustin D. Flannery

Background

Cytomegalovirus (CMV) remains a significant infection in neonates and its early detection can aid with further treatment (antiviral, audiology). However, current diagnostics do not provide genetic information.

Objective

We explored the use of the portable and comprehensive sequencing method from Oxford Nanopore Technologies, utilizing low-cost Flongle flow cells to detect and perform sequence-level characterization of neonatal urine samples that tested positive for CMV by PCR.

Study design

We performed a pilot study based on a retrospective cohort study of neonates who were positive for CMV by PCR, who were admitted at two birth hospitals in Philadelphia, PA. We leveraged deep and long-read sequencing results to analyze the reads in two forms: by comparing them against a reference-based strain and by reconstructing the genome through de novo assembly with phylogenetic tree analysis.

Results

We assayed seven clinical samples, including a positive and negative control sample, from newborns ranging from 23 weeks' gestation to term, with testing performed for microcephaly, hearing test results, small gestational age, and thrombocytopenia. Each sample showed multiple differences compared to the reference strain, and the phylogenetic tree analysis of the de novo assembly depicted the genetic diversity of the samples.

Conclusion

This pilot study shows that nanopore sequencing with low-cost Flongle flow cells can detect and characterize CMV strains from clinical neonatal urine samples. This, coupled with current screening and diagnostic criteria, could further our genomic understanding of neonatal CMV, such as viral genome diversity, genotype-phenotype associations, and spread of strains.
巨细胞病毒(CMV)在新生儿中仍然是一种重要的感染,它的早期发现有助于进一步的治疗(抗病毒,听力学)。然而,目前的诊断并不能提供遗传信息。目的:利用低成本的Flongle流式细胞对经PCR检测为巨细胞病毒阳性的新生儿尿液样本进行检测并进行序列水平的鉴定,探索牛津纳米孔技术的便携式综合测序方法。研究设计我们进行了一项基于回顾性队列研究的试点研究,这些新生儿通过PCR检测CMV阳性,他们在宾夕法尼亚州费城的两家分娩医院住院。我们利用深读和长读测序结果以两种形式分析reads:通过将它们与基于参考的菌株进行比较,以及通过系统发育树分析通过从头组装重建基因组。结果我们分析了7个临床样本,包括阳性和阴性对照样本,来自妊娠23周至足月的新生儿,进行了小头畸形、听力测试结果、小胎龄和血小板减少症的测试。与参考菌株相比,每个样品都显示出多种差异,对de novo组装的系统发育树分析描述了样品的遗传多样性。结论采用低成本Flongle流式细胞进行纳米孔测序,可以检测新生儿临床尿液中的巨细胞病毒。这与目前的筛查和诊断标准相结合,可以进一步加深我们对新生儿巨细胞病毒的基因组理解,如病毒基因组多样性、基因型-表型关联和菌株传播。
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引用次数: 0
Comparative effects of three SARS-CoV-2 inactivation methods on cytokine detection using LEGENDplex™ bead-based immunoassays 三种SARS-CoV-2灭活方法对LEGENDplex™免疫检测细胞因子的比较效果
IF 1.6 4区 医学 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-08-24 DOI: 10.1016/j.jviromet.2025.115244
Yifan Chen , Ting Zhang , Jie Zhang , Xixuan Dong , Lixiang Xue , Zhongnan Yin
In virology-related studies, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is routine to inactivate body fluid samples carrying the virus to reduce the spread of the virus and guarantee the safety of biobankers and researchers. However, inactivation treatments may affect the molecular structure of proteins in biological samples, and it is necessary to select an inactivation method that has the least impact on the target molecule associated with protein detection techniques. Cytometric Bead Array (CBA), a novel and powerful technology, allows the simultaneous quantification of up to 10–30 different soluble proteins from one sample, with a particular focus on various cytokines and chemokines in human body fluids. But only a few studies have investigated the effect of inactivation methods on relevant assays. Therefore, this study aims to investigate various viral inactivation methods and evaluate their impact on LEGENDplex™ bead-based immunoassays. By detecting eight plasma samples and eight ascites samples, we assessed the impacts of heat denaturation, γ-irradiation, and paraformaldehyde (PFA) inactivation methods on certain protein components in plasma and ascites by LEGENDplex™ bead-based immunoassays. The results showed that heat treatment and γ-irradiation treatment had little effect on LEGENDplex™ bead-based immunoassays in both blood and ascites, while PFA treatment resulted in changes in multiple cytokines and chemokines. Among twenty-six cytokines and chemokines, perforin, I-TAC (CXCL11), Eotaxin (CCL11), and MIP-3α (CCL20) were more vulnerable to heat denaturation, γ-irradiation, and PFA treatments. To sum up, our findings provide evidence to inform the selection of optimal inactivation methods for reliable cytokine profiling in SARS-CoV-2-infected samples.
在包括SARS-CoV-2在内的病毒学相关研究中,常规做法是对携带病毒的体液样本进行灭活,以减少病毒的传播,保证生物银行和研究人员的安全。然而,失活处理可能会影响生物样品中蛋白质的分子结构,与蛋白质检测技术相关,有必要选择对靶分子影响最小的失活方法。CBA是一种新颖而强大的技术,可以同时定量多达10-30种不同的可溶性蛋白质,特别关注人体体液中的各种细胞因子和趋化因子。但只有少数研究探讨了灭活方法对相关测定的影响。因此,本研究旨在研究各种病毒灭活方法,并评估它们对LEGENDplex™珠免疫测定的影响。通过检测8份血浆样品和8份腹水样品,我们采用LEGENDplex™珠免疫分析法,评估热变性、γ辐照和多聚甲醛(PFA)失活方法对血浆和腹水中某些蛋白质成分的影响。结果显示,热处理和γ辐照处理对血液和腹水中基于LEGENDplex™珠的免疫测定影响不大,而PFA处理导致多种细胞因子和趋化因子的变化。在26种细胞因子和趋化因子中,穿孔素、I-TAC (CXCL11)、Eotaxin (CCL11)和MIP-3α (CCL20)更容易受到热变性、γ辐照和PFA处理的影响。综上所述,我们的研究结果为选择最佳的失活方法提供了证据,以可靠地分析sars - cov -2感染样本的细胞因子。
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Journal of virological methods
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