Journal of virological methods最新文献

{"title":"Attenuation of viral replication foci in nuclei by 1,6 Hexanediol implicates phase separation in the assembly of baculoviral replication factories","authors":"Alexander D. Finoshin ,&nbsp;Oksana I. Kravchuk ,&nbsp;Kim I. Adameyko ,&nbsp;Anfisa S. Ryabchenko ,&nbsp;Vladimir A. Gushchin ,&nbsp;Yulia V. Lyuvpina ,&nbsp;Victor S. Mikhailov","doi":"10.1016/j.jviromet.2025.115147","DOIUrl":"10.1016/j.jviromet.2025.115147","url":null,"abstract":"<div><div>The assembly of replication factors into functional complexes is crucial for the initiation of viral genome replication and processing of nascent viral DNA. Binding to viral DNA and interaction of protein domains presumably guide compartmentalization of replication factors. The phase separation due to hydrophilicity and hydrophobicity of components may also contribute to the assembling process. However, phase separation effects are poorly investigated in the infection cycle of baculoviruses, large DNA viruses infecting Diptera, Hymenoptera, and Lepidoptera insects. Herein, we describe an investigation on a possible role of phase separation in the assembly of nuclear replication factories in <em>Spodoptera frugiperda</em> Sf9 cells infected with the Autographa californica multiple nucleopolyhedrovirus (AcMNPV). The inhibitory effect of 1,6-Hexanediol on the translocation of a viral DNA binding protein (DBP) to the replicative centers has revealed the involvement of liquid phases separation in the assembly of these centers. DBP is a structural component of the virogenic stroma, a sub-nuclear membrane-less compartment involved in viral DNA replication and the production of nucleocapsids. This sub-nuclear structure is presumably assembled via a biomolecular condensation mechanism.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115147"},"PeriodicalIF":2.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563762","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}

{"title":"Clinical validation of the Roche cobas HPV test on the Roche cobas 6800 system for the purpose of cervical screening and qualification as a second-generation comparator test","authors":"Marco Ho Ting Keung ,&nbsp;Nikita Mehta ,&nbsp;Elliott Lynn ,&nbsp;Eunice Pineda ,&nbsp;Dagnachew Fetene ,&nbsp;Alvin Lee ,&nbsp;Nick Vandegraaff ,&nbsp;Terri Sahin ,&nbsp;Alice Chynoweth ,&nbsp;Cassandra Bonney ,&nbsp;Hiu Tat Mark Chan ,&nbsp;Marc Arbyn ,&nbsp;Marion Saville ,&nbsp;David Hawkes","doi":"10.1016/j.jviromet.2025.115145","DOIUrl":"10.1016/j.jviromet.2025.115145","url":null,"abstract":"<div><div>This study assessed the relative clinical sensitivity and specificity for cervical precancer of the Roche cobas HPV test when processed using the Roche cobas 6800 system using the Roche cobas 4800 HPV test as comparator. Intra- and inter-laboratory reproducibility were evaluated as well. The cobas HPV test run on the cobas 6800 platform demonstrated a relative clinical sensitivity of 1.00 for histologically confirmed CIN2 + lesions in woman aged 30 years or older, with a relative clinical specificity of 1.001 (p for non-inferior accuracy &lt; 0.0001). The intra- and inter-laboratory reproducibility were 99.6 % and 99.8 % respectively. The study is the third to show that cobas HPV testing on the 6800 platform consistently demonstrates a relative clinical sensitivity of ≥ 0.95 and a relative clinical specificity of ≥ 0.98 for CIN2 + . This would qualify it, according to a recently published criteria, as a second-generation comparator assay.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115145"},"PeriodicalIF":2.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143577149","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}

{"title":"Evaluation of the performance of a dengue NS1 assay during the 2024 epidemic in Brazil","authors":"Cristina Mendes de Oliveira ,&nbsp;Fernanda Yoshika Takahashi ,&nbsp;Rodrigo Salazar Silva ,&nbsp;Marina Soika ,&nbsp;Juliane Nunes Ribeiro ,&nbsp;Gabriela Laginestra Francisco ,&nbsp;Vanessa Vidotto Frade de Oliveira ,&nbsp;Debora Rodrigues de Sousa ,&nbsp;José Fernando de Souza ,&nbsp;Annelise C.W. Lopes ,&nbsp;José Eduardo Levi","doi":"10.1016/j.jviromet.2025.115143","DOIUrl":"10.1016/j.jviromet.2025.115143","url":null,"abstract":"<div><div>Accurate diagnosis of dengue in the acute phase is crucial for proper patient management, reducing mortality rates, and enabling public health authorities to implement effective vector control measures. Our study, conducted during the 2024 dengue epidemic in Brazil, compared the results of a rapid dengue NS1 antigen detection assay with dengue RT-PCR using 300 serum specimens. Ninety-five percent of the patients reported symptoms consistent with dengue infection. We observed substantial agreement between the two tests (kappa = 0.8). The rapid NS1 test demonstrated 87 % sensitivity and 92.7 % specificity, using dengue RT-PCR as the gold standard. Our findings confirm that the rapid NS1 antigen detection test can be reliably used during the acute phase of dengue infection to provide an accurate diagnosis.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115143"},"PeriodicalIF":2.2,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143551531","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}

{"title":"Silymarin exerts antioxidant and antiviral effects on Zika virus infection","authors":"Rafaela Lameira Souza Lima ,&nbsp;Marília Bueno da Silva Menegatto ,&nbsp;Letícia Trindade Almeida ,&nbsp;José Carlos de Magalhães ,&nbsp;Ariane Coelho Ferraz ,&nbsp;Cintia Lopes de Brito Magalhães","doi":"10.1016/j.jviromet.2025.115133","DOIUrl":"10.1016/j.jviromet.2025.115133","url":null,"abstract":"<div><div>The Zika virus (ZIKV) – <em>Orthoflavivirus zikaense</em> – epidemic and its association with severe neurological disorders have created an urgent need to understand the disease pathogenesis and identify potential therapeutic targets. In previous investigations, we have shown that oxidative stress is associated with the pathogenesis of ZIKV infection <em>in vitro</em> and <em>in vivo</em>, and that silymarin has anti-ZIKV action <em>in vitro</em>. Here, we characterised the antioxidant and antiviral effects of silymarin against ZIKV infection in an animal model. We observed an increase in the levels of biomarkers of oxidative damage and in antioxidant enzyme activities in the livers of ZIKV-infected C57BL/6 mice. However, these effects were reversed in ZIKV-infected animals that were treated with silymarin. Furthermore, silymarin reduced the viral load in the livers of animals. Next, by <em>in vitro</em> studies, we confirmed that the anti-ZIKV action of silymarin is independent of its antioxidant activity. This work reinforces the potential use of silymarin against Zika fever.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115133"},"PeriodicalIF":2.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563760","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}

{"title":"Optimization of a panel of behavioral tests for use in containment using a golden Syrian hamster model","authors":"Rachel A. Reyna ,&nbsp;Jordyn Walker ,&nbsp;Ashley Viveros ,&nbsp;Brooke Mitchell ,&nbsp;Ennid Dulaney ,&nbsp;Divya P. Shinde ,&nbsp;Jessica A. Plante ,&nbsp;Andrew Kocsis ,&nbsp;Corrie Ntiforo ,&nbsp;Scott C. Weaver ,&nbsp;Kenneth S. Plante","doi":"10.1016/j.jviromet.2025.115132","DOIUrl":"10.1016/j.jviromet.2025.115132","url":null,"abstract":"<div><div>Golden Syrian hamsters are an often-overlooked model in behavioral testing. While previously utilized for research examining circadian rhythms and mammalian reproduction, they are less common than murine models in both infectious disease and behavioral studies. However, coronavirus disease-19 (COVID-19) quickly pushed hamster modeling to the forefront due to its myriad of advantages over mice in recapitulating human pathology and transmission. At least 10 % of COVID-19 survivors suffer from post-acute sequelae of COVID-19 (PASC), a collection of some 200 sequelae with neurologic sequelae (neuro-PASC) presenting with potentially debilitating symptomology. This presents a clear need for a small animal model that recapitulates human disease with the ability to assess any potential long term neurological changes. We adapted and optimized a panel of behavioral tests from previously accepted murine models utilizing the golden Syrian hamster model for use within biocontainment facilities. Our panel includes grip strength, Porsolt forced swim, and novel object recognition testing to measure muscle fatigue or weakness, depression, and memory loss or cognitive impairment, respectively. Apart from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), this panel of tests is applicable to other pathogens that cause neurologic sequelae, such as Nipah or eastern equine encephalitis viruses, or any other model systems that require the use of hamsters. In this manuscript, we detail the methods for each of these three behavioral tests, how to interpret and analyze the resulting data, and emphasize additional factors for consideration. We also provide baseline data for both male and female golden Syrian hamsters.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115132"},"PeriodicalIF":2.2,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567559","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}

{"title":"Evaluation of a concentration method for the recovery of human adenovirus from mineral water, tap water and well water","authors":"Nouhaila Elfellaki ,&nbsp;Salma Berrouch ,&nbsp;Simeon Goïta ,&nbsp;Hibatallah Lachkar ,&nbsp;Houda Rafi ,&nbsp;Abdelkader Biary ,&nbsp;Jamal Eddine Hafid","doi":"10.1016/j.jviromet.2025.115142","DOIUrl":"10.1016/j.jviromet.2025.115142","url":null,"abstract":"<div><div>Human adenoviruses (HAdV) are frequently excreted in large quantities and persist for extended periods in the environment, posing a significant health risk related to waterborne gastroenteritis. The objective of this study was to evaluate an adsorption-elution method using a negatively charged nitrocellulose membrane for its effectiveness in recovering HAdV from three different types of water (mineral water, tap water and well water). The detection of HAdV was carried out using real-time PCR. For this purpose, sterilized water samples were spiked with HAdV-infected stool and filtered through an electronegative membranes coated with MgCl₂ to retain viral particles. Subsequently, the viruses were eluted from the filters using sodium hydroxide and concentrated through two centrifugation cycles. Viral nucleic acids were then extracted and detected by real time PCR. Regarding HAdV recovery, the method's efficiency varied depending on the type of analyzed water. However, this method demonstrated a consistent performance, providing reliable results across different water samples, whether from mineral water, tap water or well water. This consistency in viral recovery is crucial to ensuring the accuracy and reliability of virological analyses in various aquatic environments.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115142"},"PeriodicalIF":2.2,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563761","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}

{"title":"A newly developed whole genome sequencing protocol enables early tracking of enterovirus D68 molecular evolution","authors":"Federica AM Giardina ,&nbsp;Greta Romano ,&nbsp;Guglielmo Ferrari ,&nbsp;Laura Pellegrinelli ,&nbsp;Arlinda Seiti ,&nbsp;Cristina Galli ,&nbsp;Elena Pariani ,&nbsp;Fausto Baldanti ,&nbsp;Antonio Piralla","doi":"10.1016/j.jviromet.2025.115131","DOIUrl":"10.1016/j.jviromet.2025.115131","url":null,"abstract":"<div><h3>Background</h3><div>Human enterovirus D68 (EV-D68) has been associated with an increase in mild-to-severe pediatric respiratory diseases worldwide. The rate of circulation of this virus is largely underestimated in the population and genetic evolutionary data are usually available only for partial sequences. To achieve a timely genomic surveillance, a reliable, high-throughput EV-68 sequencing assay is required. Here we report an improved high-throughput EV-D68 whole-genome sequencing assay performed directly on clinical samples that is suitable for short-read sequencing platforms. Between June and December 2022, a total 37 (1.9 %) respiratory samples were EV-D68 positive and together with 52 additional samples with a median cycle of quantification (Cq) of 28.3, ranging from 18 to 36.8 Cq were included in the validation analyses. Overall, all the primers had good performance and no mismatches were detected in more than 85 % of sequences (932 whole-genome dataset). Using a cut-off of Cq &lt; 32 in at least 85.5 % of samples a whole-genome or partial genome was obtained, confirming an acceptable positive sequencing rate for the designed method. A total of 65 whole-genome sequences were obtained and have a mean coverage of 98.4 % across the genome, with a median depth of 6158x (range 2815x-7560x). Based on the obtained data, this method is cost effective resulting in an easy-to-perform protocol helpful for tracing the evolution of EV-D68 in protein different from VP1. EV-D68 could become a significant pathogen for public health in the next future, and thus this protocol for whole genome sequencing could help clinical and molecular virologists to be ready for molecular epidemiology surveillance.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115131"},"PeriodicalIF":2.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143512081","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}

{"title":"Comparison of sample pretreatments used to distinguish between infectious and non-infectious foodborne viruses by RT-qPCR","authors":"Anne-Marie Lauzier ,&nbsp;Émilie Douette ,&nbsp;Antoine Labrie ,&nbsp;Éric Jubinville ,&nbsp;Valérie Goulet-Beaulieu ,&nbsp;Fabienne Hamon ,&nbsp;Julie Jean","doi":"10.1016/j.jviromet.2025.115130","DOIUrl":"10.1016/j.jviromet.2025.115130","url":null,"abstract":"<div><div>To detect viruses such as hepatitis A virus (HAV) and human norovirus (HuNoV) in foods, RT-qPCR or other molecular methods are used, which cannot distinguish between infectious and non-infectious virions. Samples can be pretreated to limit detection to intact and presumably infectious virions. We compared propidium monoazide (PMA or PMAxx), platinum (IV) chloride (PtCl₄), magnetic silica beads and centrifugal filter using HAV or HuNoV inactivated by heat, pulsed light, or sodium hypochlorite (NaOCl). PMAxx completely or nearly eliminated (3.96 ± 1.24 log gc) the RT-qPCR signal of HAV inactivated at 100°C for 10 min. Pretreatments could not reduce significantly RT-qPCR signal of HAV after pulsed light (0.74 ± 0.36 log gc) and NaOCl (0.24 ± 0.14 log gc) inactivation. Enzymatic treatments did not improve the results obtained with PMAxx. The exudate of raspberry, strawberry or oyster used as food matrices needed dilution by at least tenfold for PMAxx to to yield results comparable to virions without a food matrix. Overall, PMAxx shows good potential to discriminate between infectious and non-infectious despite some remaining limitations.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"335 ","pages":"Article 115130"},"PeriodicalIF":2.2,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492617","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}

{"title":"Critical parameters on Zika virus-like particles’ generation","authors":"Vinícius Aragão Tejo Dias ,&nbsp;Ana Luiza Moraes Octaviano ,&nbsp;Júlia Públio Rabello ,&nbsp;Fernanda Angela Correia Barrence ,&nbsp;Thaissa Consoni Bernardino ,&nbsp;Jaci Leme ,&nbsp;Soraia Attie Calil Jorge ,&nbsp;Eutimio Gustavo Fernández Núñez","doi":"10.1016/j.jviromet.2025.115129","DOIUrl":"10.1016/j.jviromet.2025.115129","url":null,"abstract":"<div><div>The Zika virus became a global threat in 2015 due to its association with microcephaly. Preventing its spread depends on developing vaccines, with virus-like particles (VLP) being a promising approach, especially because of their safety profile and high immunogenicity. This study focused on the production of Zika VLP using Sf9 cells and the baculovirus expression system, evaluating cell growth kinetics, nutrient consumption, and metabolite production in Sf-900™ III medium. As a methodology, this study includes bioreactor experiments, cell density and viability quantification, nutrient and metabolite analysis, Dot Blot, Western Blot, and transmission electron microscopy. Among the critical conditions tested are culture medium supplementation with 0.028 mM cholesterol/ 6 nM bovine serum albumin, multiplicity of infection (MOI= 0.2 or 2), and dissolved oxygen tension (DOT= 5 or 30 % air saturation). As a result, in the growth phase, Sf9 cells achieved rapid exponential growth, with doubling times ranging from 22.8 to 35.4 hours and standard nutrient consumption and metabolite generation profiles for this cell line. The infection phase recorded cell death rates between 8200 and 12600 cells mL⁻¹ h⁻¹ , with higher VLP production under low MOI (0.2) and low DOT (5 %). These conditions also reduced protein degradation and nutrient consumption. The produced VLP ranged from 32 to 73 nm in size, with smaller sizes observed under low MOI conditions. Finally, controlling the DOT at 5 % air saturation without cholesterol/albumin supplementation increased VLP production without the need to raise the viral load, highlighting the importance of choosing the appropriate combination of critical parameters (MOI, DOT, and medium supplementation) as key factors in optimizing the upstream process. This finding impacts substantially upstream stage efficiency and economy, which could be useful for future scaling up to the commercial manufacturing scale.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"334 ","pages":"Article 115129"},"PeriodicalIF":2.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468074","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}

{"title":"Evaluation of inactivated snakehead rhabdovirus as an internal positive control for RT-qPCR diagnosis of viral hemorrhagic septicemia virus in fish","authors":"Myoung Gwang Choi ,&nbsp;Do-Hyung Kim ,&nbsp;Hyoung Jun Kim ,&nbsp;Ki Hong Kim","doi":"10.1016/j.jviromet.2025.115128","DOIUrl":"10.1016/j.jviromet.2025.115128","url":null,"abstract":"<div><div>Viral hemorrhagic septicemia virus (VHSV) is a significant pathogen causing mass mortalities in marine and freshwater fish worldwide. Accurate diagnosis through quantitative reverse transcription PCR (RT-qPCR) is essential to prevent its spread, but false negatives can compromise results. In this study, we evaluate the use of heat-inactivated snakehead rhabdovirus (SHRV) as an internal positive control (IPC) for VHSV diagnosis. SHRV's similarity to VHSV in viral structure and genome makes it an ideal IPC. The introduction of SHRV IPC into the RT-qPCR workflow can improve the reliability of diagnostic results by enabling the detection of technical failures during the RNA extraction or amplification process. Our results show that heat-inactivated SHRV preserved RNA integrity for IPC use, and SHRV IPC can provide a useful tool for detecting and interpreting false negatives without affecting assay sensitivity.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"334 ","pages":"Article 115128"},"PeriodicalIF":2.2,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143430148","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}