Abstract:
:West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity.
journal_name
J Virol Methodsjournal_title
Journal of virological methodsauthors
Kolekar P,Hake N,Kale M,Kulkarni-Kale Udoi
10.1016/j.jviromet.2013.12.012subject
Has Abstractpub_date
2014-03-01 00:00:00pages
41-55eissn
0166-0934issn
1879-0984pii
S0166-0934(13)00514-4journal_volume
198pub_type
杂志文章abstract::28 isolates of canine parvovirus type-2 (CPV-2) were obtained from dogs with hemorrhagic gastroenteritis in Italy. The antigenic structure of CPV-2 isolates was characterized, using four discriminating monoclonal antibodies. In addition, four vaccinal strains were examined. Similar to reports from Australia and the Un...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(98)00055-x
更新日期:1998-08-01 00:00:00
abstract::Human cytomegalovirus (HCMV) is the most common cause of congenital viral infection in the developed world, and can lead to significant morbidity. Animal models of HCMV infection are required for study of pathogenesis, because of the strict species-specificity of cytomegalovirus (CMV). Among the small animal CMV model...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(02)00265-3
更新日期:2003-03-01 00:00:00
abstract::We describe a laboratory information system employing a virus and chlamydia database developed over seven years which is used by a regional laboratory, performing virus and chlamydia testing. The information system is implemented on a University mainframe computer and accessed by computer terminals in the laboratory. ...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(89)90108-0
更新日期:1989-12-01 00:00:00
abstract::Detection of classical swine fever virus (CSFV) and its discrimination from other pestiviruses can be achieved by virus isolation (VI) in cell cultures, antigen detection, or molecular analysis. To simplify the latter, a 5'-nuclease assay (TaqMan) was developed for the rapid and specific detection of CSFV with the min...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(97)00208-5
更新日期:1998-06-01 00:00:00
abstract::Contaminated recreational waters pose a public health concern, as the potential for waterborne diseases exists in water contaminated with human fecal waste. Worldwide, bacterial indicators such as Escherichia coli, enterococci, and total and fecal coliform are used as indicators of water quality. However, enteric viru...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2013.06.028
更新日期:2013-11-01 00:00:00
abstract::Xenotropic murine leukemia virus (X-MuLV) is often used in retrovirus elimination studies involving rodent cells. Currently, X-MuLV is measured using a focus-forming assay on mink (MiCl1 S+L-) or cat (PG-4 S+L-) cell lines. An easier and quicker PG-4 cell plaque assay, which retains the statistical reproducibility of ...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(99)00064-6
更新日期:1999-08-01 00:00:00
abstract::Mammalian orthoreoviruses (reoviruses) have served as highly useful models for studies of virus replication and pathogenesis. The development of a plasmid-based reverse genetics system represented a major breakthrough in reovirus research. The current reverse genetics systems for reoviruses rely on the expression of T...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2013.10.023
更新日期:2014-02-01 00:00:00
abstract::Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed livestock which has a drastic economic impact for affected countries. Although FMDV is distributed worldwide, many regional programs have been effective eradicating this agent. In Argentina, as in many other regions of South America, the comb...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2011.09.011
更新日期:2011-12-01 00:00:00
abstract::Porcine endogenous retroviruses (PERV) represent a risk for xenotransplantation using pig cells, tissues or organs. PERV-A and PERV-B are present in the genome of all pigs and both infect human cells in vitro. PERV-C infects only pig cells and it is integrated in the genome of most, but not all pigs. Recombinants betw...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2011.04.017
更新日期:2011-07-01 00:00:00
abstract::A chimeric porcine circovirus (PCV) 1-2b vaccine strain and its parental wild-type PCV2b strain from China (PCV2-J) were used separately to vaccinate BALB/c mice and tissue and serum samples were collected from the mice to investigate whether the replication properties of the viruses differed. The spleen lymphocytes f...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2020.113905
更新日期:2020-09-01 00:00:00
abstract::Two methods for denaturing double stranded (ds)RNA of infectious bursal disease virus for the purpose of reverse transcribing it were compared: Heat denaturation at 65 degrees C in the presence of DMSO and in the absence of DMSO. As part of the analysis, the nature of cDNA in the two preparations was examined by polym...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(94)90081-7
更新日期:1994-04-01 00:00:00
abstract::The species cowpox virus (CPXV), genus Orthopoxvirus (OPV), consists of isolates highly variable in their biological properties and their genotypes. A TaqMan PCR assay for the specific detection of CPXV DNA based on sequences of the ORF D11L has been developed recently. (Gavrilova et al., 2010; Shchelkunov et al., 201...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2014.10.004
更新日期:2015-01-01 00:00:00
abstract::Sample preparation is an important step in the detection of viral DNA by the polymerase chain reaction (PCR) technique. The method used should achieve release of cellular DNA with the minimum of manipulation steps so as to reduce the possibility of contamination. The present report demonstrates that either microwaving...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(93)90009-g
更新日期:1993-09-01 00:00:00
abstract::Potato spindle tuber viroid (PSTVd) is a quarantine pathogen in the European Union and causes damaging diseases of solanaceous crops. Under the EU Plant Health directive 2000/29/EC, countries must have the ability to detect and identify accurately and rapidly the introduction of harmful organisms in plants or plant pr...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2003.11.005
更新日期:2004-03-15 00:00:00
abstract::A colloid gold strip (CGS) test for detecting antibodies to H5 subtype Avian Influenza Virus (AIV) was developed. The test is based on membrane chromatography and uses colloidal gold conjugated with inactivated AIV-H5N1 as the tracer. On the test strip, a baculovirus expressed haemagglutinin (HA) protein was used as t...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2008.06.011
更新日期:2008-09-01 00:00:00
abstract::The polymerase chain reaction (PCR) is one of the most efficient techniques for measuring the viral load of HIV-infected samples. Determination of the specificity of PCR products is usually based on Southern blotting and hybridization of the amplified DNA to radioactive oligonucleotide probes specific for sequences co...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(94)90028-0
更新日期:1994-05-01 00:00:00
abstract::Peste des petits ruminants (PPR) is a viral disease of small ruminants that is caused by the PPR virus (PPRV) and is a significant burden on subsistence farmers across the developing world. Loop-mediated isothermal amplification (LAMP) provides cost-effective, rapid, specific and sensitive detection of nucleic acid an...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2019.113730
更新日期:2019-12-01 00:00:00
abstract::A new system for inoculation of plants with begomoviral DNA without cloning or the use insect vectors is described. Total DNA extracted from begomovirus-infected plants was amplified by rolling circle amplification (RCA) using the bacteriophage phi29 DNA polymerase, and inoculated to plants by particle bombardment. In...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2010.04.022
更新日期:2010-09-01 00:00:00
abstract::The Cucumber mosaic virus (CMV) is an isodiametric plant virus with an extremely wide host range, present worldwide. CMV chimeric particles (R9-CMV), engineered to express a 27-aa synthetic peptide derived from Hepatitis C virus (HCV), were demonstrated to be stable under simulated gastric and intestinal conditions. T...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2010.01.021
更新日期:2010-05-01 00:00:00
abstract::In this study, we aim to determine what effects prolonged storage and repeated freeze/thaw cycles have on the stability of influenza A(H1N1)pdm09 (influenza A/H1N1)RNA. Cloned influenza A/H1N1 RNA transcripts were serially diluted from 8.0-1.0 log10 copies/μl. RT-qPCR was used to measure RNA loss in transcripts stored...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2017.05.018
更新日期:2017-09-01 00:00:00
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journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(95)00040-2
更新日期:1995-09-01 00:00:00
abstract::Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Accurate, rapid and simple detection of CDV is critical to improve disease management and prevent outbreaks. In this study, a visible and incubation instrument-fr...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2018.07.007
更新日期:2018-10-01 00:00:00
abstract::A new, versatile baculovirus vector was developed for the generation of recombinants in the yeast Saccharomyces cerevisiae and for the expression of foreign proteins in both insect larvae and in insect cells. This vector is based on Autographa californica multiple nucleocapsid nucleopolyhedrovirus (AcMNPV) and exploit...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(97)00109-2
更新日期:1997-10-01 00:00:00
abstract::Sequence analysis of duck plague virus (DPV) revealed that there was a 528bp (B fragment) deletion within the UL2 gene of DPV attenuated vaccine strain in comparison with field virulent strains. The finding of gene deletion provides a potential differentiation test between DPV virulent strain and attenuated strain bas...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2017.08.021
更新日期:2017-11-01 00:00:00
abstract::In this study, we generated recombinant virus-like particles (VLPs) against family Filoviridae, genus Ebolavirus, species Zaire ebolavirus, strain Makona (EBOV) in Drosophila melanogaster Schneider 2 (S2) cells using the EBOV Makona. S2 cells were cotransfected with four viral plasmids encoding EBOV Makona proteins an...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2018.08.016
更新日期:2018-11-01 00:00:00
abstract::Nucleotide sequence studies detected a double-point mutation in the genomic RNA segment 4 (nt 871 and 872) of the persistent variant C/AA-pi of influenza C/Ann Arbor/1/50 virus. The 3'-end-points of two distinct PCR primers were positioned exactly at this genome location and thereby adjusted the priming determinant co...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(94)00159-e
更新日期:1995-03-01 00:00:00
abstract::One first generation assay (manufactured by Ortho, test I) and 3 second generation anti-HCV ELISAs (manufactured by Ortho, Abbott, and UBI, tests II-IV) were compared. Sera from 4 different sources were used: (1) intravenous drug-users (IVDUs, n = 50), (2) blood donors (n = 1055), (3) all clinical samples from one day...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/0166-0934(92)90087-t
更新日期:1992-12-01 00:00:00
abstract::Healthcare workers (HCWs) are at significantly higher risk of exposure to influenza virus during seasonal epidemics and global pandemics. During the 2009 influenza pandemic, some healthcare organizations recommended that HCWs wear respiratory protection such as filtering facepiece respirators, while others indicated t...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2018.05.009
更新日期:2018-10-01 00:00:00
abstract::Nucleic acid amplification techniques have become the mainstay for ultimate sensitivity for detecting low levels of virus, including human immunodeficiency virus (HIV). As a sophisticated technology with relative expensive reagents and instrumentation, adoption of nucleic acid testing (NAT) can be cost inhibited in se...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/j.jviromet.2012.08.017
更新日期:2013-03-01 00:00:00
abstract::A method for quantitative analysis of the growth properties of human cytomegalovirus (HCMV) in various cell culture systems was developed. Recent HCMV isolates are, in most cases cell associated, causing only limited cytopathic effect. This renders comparative analysis of the biological properties of such isolates dif...
journal_title:Journal of virological methods
pub_type: 杂志文章
doi:10.1016/s0166-0934(97)02082-x
更新日期:1997-01-01 00:00:00