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Journal of Virological Methods

Jens M Warnecke, Erik Lattwein, Sandra Saschenbrecker, Winfried Stöcker, Wolfgang Schlumberger, Katja Steinhagen
Zika virus (ZIKV) is a mosquito-borne flavivirus posing a public health threat due to its association with neurological complications in newborns and adults. In flavivirus-endemic areas, coming mosquito seasons will require the differentiation of primary versus secondary and acute versus past ZIKV/flavivirus infections. This is complicated by two major difficulties: [i] secondary infections often present with low or undetectable titres of specific IgM and early-positive IgG, [ii] previous flavivirus infection(s) or vaccinations cause elevated cross-reactivities...
February 16, 2019: Journal of Virological Methods
C Gómez-Aix, C Alcaide, P Gómez, M A Aranda, M A Sánchez-Pina
In situ hybridization (ISH) is an informative and relatively accessible technique for the localization of viral genomes in plant tissue and cells. However, simultaneous visualization of related plant viruses in mixed infections may be limited by the nucleotide similarity in the genomes and the single chromogenic detection over the same sample preparation. To address this issue, we used two Pepino mosaic virus isolates and performed ISH over consecutive serial cross-sections of paraffin-embedded leaf samples of single and mixed infected Nicotiana benthamiana plants...
February 13, 2019: Journal of Virological Methods
Arash Razmi, Arezoo Golestanipour, Maryam Nikkhah, Abdolreza Bagheri, Masoud Shamsbakhsh, Saeed Malekzadeh-Shafaroudi
Current techniques for plant virus detection, such as RT- PCR and ELISA, require multistep procedures and rely on sophisticated equipment. Due to the global spread of plant viruses, the development of simpler, faster and cheaper assay methods is inevitable. Gold nanoparticles (AuNPs) had raised much interest during recent years due to their novel optical properties or diagnostic purposes. The localized surface plasmon resonance (LSPR1 ) of AuNPs had been used in the development of novel colorimetric nano-biosensing systems...
February 13, 2019: Journal of Virological Methods
Andrea Hauser, Matthias An der Heiden, Karolin Meixenberger, Orjin Han, Stefan Fiedler, Kirsten Hanke, Uwe Koppe, Alexandra Hofmann, Viviane Bremer, Barbara Bartmeyer, Claudia Kuecherer, Norbert Bannert
Serological methods to differentiate between recently acquired and established HIV-1 infections are a useful tool in the HIV-surveillance to characterize the epidemic, identify groups at risk and assess HIV-preventive interventions. Therefore, an avidity-based, modified BioRad GenscreenTM HIV-1/2 assay (BRAEUR ) was evaluated according to the avidity-based, modified BioRad HIV-1/2 Plus O protocol (BRAUSA ). Overall, 692 well defined samples (82.5% B and 17.5% non-B subtypes) from recent (<180 days, n=239), intermediate (181-364 days, n=35) or long term infections (≥365 days, n=419) were used to determine a 'mean duration of recent infectioń (MDRI), a 'median DRÍ (MdDRI), the false recent rate (FRR), and concordance between the BRAs and the Sedia BED-CEIA (BED)...
February 7, 2019: Journal of Virological Methods
Jennifer L Cannon, Marian Baker, Leslie Barclay, Jan Vinjé
Noroviruses are recognized as the leading cause of acute gastroenteritis globally. With improved molecular diagnostics developed over the last two decades, archived clinical specimens are increasingly used to investigate the historic prevalence and molecular epidemiology of human norovirus. Yet the impact of long-term storage on viral integrity in clinical specimens has not been evaluated. In this study, we retested 994 stool specimens collected between 1996 and 2017 that originally tested norovirus-positive to quantify the loss of norovirus RT-PCR positivity with increasing sample storage time at 4°C...
February 5, 2019: Journal of Virological Methods
Rochelle Rademan, Wanda Markotter, Janusz T Paweska, Petrus Jansen Van Vuren
Zika (ZIKV) and Spondweni viruses (SPOV) are closely related mosquito borne flaviviruses in the Spondweni serogroup. The co-circulation and similar disease presentation following ZIKV and SPOV infection necessitates the development of a diagnostic tool for their simultaneous detection and distinction. We developed a one-step multiplex real-time RT-PCR (ZIKSPOV) to detect and distinguish between SPOV and ZIKV by utilizing a single primer set combined with virus specific hydrolysis probes. The ZIKSPOV assay was compared to published virus specific real-time RT-PCR assays and the limit of detection was comparable...
February 4, 2019: Journal of Virological Methods
Antoinette van Schalkwyk, Maryke Louise Ferreira, Marco Romito
A new Reverse Transcription - Polymerase Chain Reaction (RT-PCR) assay is described that can differentiate between the nine serotypes of African horse sickness virus (AHSV). A unique set of primers targeting regions in the corresponding genome segment-2 were designed for each serotype. Sequences of the individual amplicons have single nucleotide polymorphisms (SNPs) allowing discrimination between field samples and either reference strains or live attenuated viruses (ALVs). This assay was tested and used to determine the serotype prevalence of AHSV samples submitted during the 2016 / 2017 season as well as to determine the incidence of field samples derived from ALVs...
February 2, 2019: Journal of Virological Methods
Miaolei Li, Jian Zu
Understanding the infection and pathogenesis mechanism of hepatitis B virus (HBV) is very important for the prevention and treatment of hepatitis B. Mathematical models contribute to illuminate the dynamic process of HBV replication in vivo. Therefore, in this paper we review the viral dynamics in HBV infection, which may help us further understand the dynamic mechanism of HBV infection and efficacy of antiviral treatment. Firstly, we introduce a family of deterministic models by considering different biological mechanisms, such as, antiviral therapy, CTL immune response, multi-types of infected hepatocytes, time delay and spatial diffusion...
February 1, 2019: Journal of Virological Methods
Madhuri S Joshi, Shital G Deore, Atul M Walimbe, Sujata S Ranshing, Shobha D Chitambar
The nucleotide alignment of all 11 genes of human Rotavirus A (RVA) strains revealed suitability of NSP2, NSP3 and VP6 genes for the development of real time PCR (qRT-PCR). Evaluation of qRT-PCR assays using known rotavirus ELISA positive and negative fecal specimens showed non-overlapping ranges of Mean ±3SD cycle threshold (Ct) values for NSP3 and VP6 based assays. Using serial dilutions of purified RVA, high sensitivity of VP6qRT-PCR assay (1.95 × 10-5 pg/µL of RNA) was recorded as compared to NSP2 and NSP3 qRT-PCR assays (1...
January 30, 2019: Journal of Virological Methods
Xingang Xu, Feng Yang, Qi Zhang, Ying Xu, Jiali Huang, Mingzhe Fu, Weimin Zhang
Mixed infections with different pathogens are common in sheep and goats under intensive production conditions. Quick and accurate detection and differentiation of different pathogens is necessary for epidemiological surveillance, disease management and import and export controls. Multiplex TaqMan qPCR protocols were developed and subsequently evaluated as effective tools in simultaneously detecting single and mixed infections in sheep and goats. Four pairs of primers and four probes labeled with Rox/BHQ2, Cy5/BHQ2, Hex/BHQ1 and Fam/BHQ1 for peste des petits ruminants virus (PPRV), foot and mouth disease virus (FMDV), goat pox virus (GTPV) and orf virus (ORFV), respectively, were used in the multiplex TaqMan qPCR assay...
January 28, 2019: Journal of Virological Methods
Sheng-Wen Huang, Su-Jhen Hung, Jen-Ren Wang
The first deep sequencing method was announced in 2005. Due to an increasing number of sequencing data and a reduction in the costs of each sequencing dataset, this innovative technique was soon applied to genetic investigations of viral genome diversity in various viruses, particularly RNA viruses. These deep sequencing findings documented viral epidemiology and evolution and provided high-resolution data on the genetic changes in viral populations. Here, we review deep sequencing platforms that have been applied in viral quasispecies studies...
January 25, 2019: Journal of Virological Methods
Maria Teresa Scicluna, Gian Luca Autorino, Sheila J Cook, Charles J Issel, R Frank Cook, Roberto Nardini
Equine infectious anaemia (EIA) is a blood borne disease that is listed among the notifiable diseases of the World Organisation for Animal Health (OIE). EIA is also regulated by the OIE for the international trading provisions and is generally subject to control programmes. Since 2011, Italy has been conducting a surveillance plan based on a three-tier diagnostic system, using a serological ELISA as screening test, an agar gel immunodiffusion test (AGIDT) as a confirmatory method, and an immunoblot (IB) as an alternative confirmatory assay for discordant results between the first two tests...
January 23, 2019: Journal of Virological Methods
Daniel Wüthrich, Daniela Lang, Nicola F Müller, Richard A Neher, Tanja Stadler, Adrian Egli
We compared two sample preparation protocols for whole genome sequencing of influenza A viruses. Each protocol was assessed using cDNA quantity and quality and the resulting mean genome coverage after sequencing. Both protocols produced acceptable result for samples with high viral load, whereas one protocol performed slightly better with limited virus count.
January 21, 2019: Journal of Virological Methods
Wen-Jun Liu, You-Tian Yang, Si-Min Du, Hua-Dong Yi, Dan-Ning Xu, Nan Cao, Dan-Li Jiang, Yun-Mao Huang, Yun-Bo Tian
Goose parvovirus (GPV) is one of the most serious viral pathogens in goslings. Recently, a new pathogen to the Chinese mainland-duck-origin novel goose parvovirus (N-GPV)-was found to be 90.8-94.6% identical to the nucleotide sequence of GPV, and typically causes growth disorders and high infection rates in meat ducks. The spread of both of these viruses hinders the healthy development of the waterfowl breeding industry. In this study, recombinase polymerase amplification (RPA) was combined with a vertical flow (VF) visualization strip to develop a universal assay for the rapid detection of GPV and N-GPV...
January 21, 2019: Journal of Virological Methods
Alexander P Ivanov, Tatiana D Klebleyeva, Lyudmila P Malyshkina, Olga E Ivanova
The first application results of enzyme immunoassay system (ELISA) - binding inhibition ELISA (BI ELISA) for the detection of antibodies to polioviruses of three types based on the use of specific antibodies from chicken yolk (IgY) are presented. This variant of ELISA is a "surrogate" neutralization test (NT). When comparing the results of the detection of antibodies in 90 sera of children who were vaccinated with oral and inactivated poliovirus vaccines, good correlation (r = 0.67, 0.61, 0.76 for types 1, 2, 3 respectively) between the BI ELISA and the NT results was shown...
January 17, 2019: Journal of Virological Methods
Ibrahim Ahmed Hamza, Kyle Bibby
Waterborne diseases have significant public health and socioeconomic implications worldwide. Many viral pathogens are commonly associated with water-related diseases, namely enteric viruses. Also, novel recently discovered human-associated viruses have been shown to be a causative agent of gastroenteritis or other clinical symptoms. A wide range of analytical methods is available for virus detection in environmental water samples. Viral isolation is historically carried out via propagation on permissive cell lines; however, some enteric viruses are difficult or not able to propagate on existing cell lines...
January 16, 2019: Journal of Virological Methods
L Busson, M Bartiaux, S Brahim, D Konopnicki, N Dauby, M Gérard, P De Backer, K Van Vaerenbergh, B Mahadeb, M De Foor, M Wautier, O Vandenberg, P Mols, J Levy, M Hallin
No abstract text is available yet for this article.
January 15, 2019: Journal of Virological Methods
E Beaver-Kanuya, S A Szostek, S J Harper
Apple stem grooving virus (ASGV) and Apple green crinkle-associated virus (AGCaV) negatively impact production, maintenance, and distribution of apples and other Malus species world-wide. Due to the increasing diversity of isolates found by high-throughput sequencing, we have developed real-time RT-qPCR assays for these two viruses. Primers and probes were designed against alignments of representative extant sequences from around the world, and reaction conditions optimized for sensitivity and specificity. Assays were validated against a panel of virus isolates, and compared to extant endpoint RT-PCR and ELISA assays...
January 13, 2019: Journal of Virological Methods
D Koontz, S Dollard, S Cordovado
BACKGROUND: Dried blood spots (DBS), collected universally from newborns in the U.S., could be used as a matrix for the detection of cytomegalovirus (CMV) infection in infants. However, sensitivity to detect CMV in DBS as compared to saliva and urine is variable across studies largely due to the DNA extraction method. Thermal shock, a widely used DNA extraction method, is highly sensitive for the detection of CMV in DBS, however, the processing time required is not practical for high-throughput testing...
January 10, 2019: Journal of Virological Methods
Lauro Velazquez-Salinas, Steven J Pauszek, Jose Barrera, Benjamin A Clark, Manuel V Borca, Antonio Verdugo-Rodriguez, Carolina Stenfeldt, Jonathan Arzt, Luis L Rodriguez
This study reports the use of a site-specific recombination cloning technique for rapid development of a full-length cDNA clone that can produce infectious vesicular stomatitis New Jersey virus (VSNJV). The full-length genome of the epidemic VSNJV NJ0612NME6 strain was amplified in four overlapping cDNA fragments which were linked together and cloned into a vector plasmid by site-specific recombination. Furthermore, to derive infectious virus, three supporting plasmid vectors containing either the nucleoprotein (N), phosphoprotein (P) or polymerase (L) genes were constructed using the same cloning methodology...
January 9, 2019: Journal of Virological Methods
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