当前位置： SCI文献检索 > JOURNAL OF VIROLOGICAL METHODS期刊下所有文献 > A novel next generation sequencing assay as an alternative to currently available methods for hepatitis C virus genotyping.

A novel next generation sequencing assay as an alternative to currently available methods for hepatitis C virus genotyping.

Abstract：

:Chronic HCV infection is one of the leading causes of liver-related death and in many countries it is a primary reason for having a liver transplant. HCV genotype identification has long been used in the clinical practice, since different genotypes have different response rates and required different doses and durations of IFN/RBV treatment; moreover both the frequency and the pattern of resistance to different Direct-Acting Antivirals (DAAs) classes are subtype specific. Hence the necessity to make an accurate HCV subtyping becomes a fundamental tool to optimize current and future clinical management of HCV infected subjects. In the present study the performance of a next generation sequencing (NGS: based on the Ion Torrent Platform-Vela Sentosa SQ 301 sequencer) HCV genotyping assay has been evaluated. The current method targets a region of the NS5B gene and it is the unique NGS based market CE-IVD assay. As a comparative method a commercial method based on the detection via reverse hybridization of 5'UTR and core regions (Versant HCV Genotype 2.0 Assay, LiPA, Siemens) was selected. A total 207 plasma samples from HCV infected individuals were used. No selection was made for these samples that were submitted for routine HCV genotyping. The results show Vela NGS assay assigns major number of HCV subtypes with respect LiPA. Concerning genotype 1 and 3, the discrepancy of assigned subtypes for LiPA with respect to Vela NGS assay is not relevant (1.8% and 2%, respectively); in contrast, the difference of assigned subtypes for genotypes 2 and 4 is very high (96.6% and 100%, respectively). The resistance mutations data, except for 1a and 1b subtypes, remain scarce; the future relevant challenge will be to identify subtypes-specific drug resistance mutations, which are essential to create highly personalized therapeutic pathways.

journal_name

J Virol Methods

journal_title

Journal of virological methods

authors

Dirani G,Paesini E,Mascetra E,Farabegoli P,Dalmo B,Bartolini B,Garbuglia AR,Capobianchi MR,Sambri V

doi

10.1016/j.jviromet.2017.10.005

subject

Has Abstract

pub_date

2018-01-01 00:00:00

pages

88-91

eissn

0166-0934

issn

1879-0984

pii

S0166-0934(17)30288-4

journal_volume

251

pub_type

杂志文章

相关文献

JOURNAL OF VIROLOGICAL METHODS文献大全
  • Epitope mapping of the NS4 and NS5 gene products of hepatitis C virus and the use of a chimeric NS4-NS5 synthetic peptide for serodiagnosis.

    abstract：:Specific domains of the NS4 and NS5 gene products of hepatitis C virus have been identified using hydrophilicity profiles for the prediction of potential immunogenic regions, and epitope scanning techniques. Peptides synthesised on the basis of such data show excellent reactivity in the ELISA format. Introduction of a...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/0166-0934(95)00060-8

    authors： Rosa C,Osborne S,Garetto F,Griva S,Rivella A,Calabresi G,Guaschino R,Bonelli F

    更新日期：1995-10-01 00:00:00

  • Evaluation of viral-lysate enzyme-linked immunosorbent assay kits for detecting human immunodeficiency virus (type 1) infections using human sera standardized by quantitative western blotting.

    abstract：:The first generation of proprietary reagents for detecting antibodies to the Human Immunodeficiency Virus Type 1 (HIV-1) by enzyme-linked immunosorbent assay (ELISA) used as antigen partially purified virus from cell culture lysates. These tests, which are still in use, may vary in their antibody measurement capabilit...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/0166-0934(92)90028-c

    authors： Hardy CT,Damrow TA,Villareal DB,Kenny GE

    更新日期：1992-06-01 00:00:00

  • Assessment of influenza virus exposure and recovery from contaminated surgical masks and N95 respirators.

    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

    authors： Blachere FM,Lindsley WG,McMillen CM,Beezhold DH,Fisher EM,Shaffer RE,Noti JD

    更新日期：2018-10-01 00:00:00

  • A sensitive assay for detection and measurement of neutralising antibody to human immunodeficiency virus.

    abstract：:An assay based on the inhibition of syncytium formation in C8166 cells was developed to measure low levels of neutralising antibody (NT-AB) to human immunodeficiency virus (HIV) and to detect cross-reactivity between virus strains. The relationship between virus challenge and antibody titre was represented by a tripar...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/0166-0934(92)90121-s

    authors： Osborne R,Mason H,Browning M,Mitchell R,Jarrett W

    更新日期：1992-09-01 00:00:00

  • Rapid diagnostic detection of plum pox virus in Prunus plants by isothermal AmplifyRP(®) using reverse transcription-recombinase polymerase amplification.

    abstract：:Plum pox virus (PPV) causes the most destructive viral disease known as plum pox or Sharka disease in stone fruit trees. As an important regulated pathogen, detection of PPV is thus of critical importance to quarantine and eradication of the spreading disease. In this study, the innovative development of two AmplifyRP...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2014.06.026

    authors： Zhang S,Ravelonandro M,Russell P,McOwen N,Briard P,Bohannon S,Vrient A

    更新日期：2014-10-01 00:00:00

  • Screening of herpes simplex virus type 1 isolates for acyclovir resistance using DiviTum® assay.

    abstract：:Rapid alternative methods are required to evaluate easily acyclovir (ACV) sensitivity of clinical herpes simplex virus (HSV) isolates. The objective of this study was to screen 54 ACV-sensitive and 41 ACV-resistant clinical HSV-1 isolates, well characterized by phenotypic and genotypic methods, for the phosphorylation...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2012.12.001

    authors： Sauerbrei A,Vödisch S,Bohn K,Schacke M,Gronowitz S

    更新日期：2013-03-01 00:00:00

  • RNAlater® is a viable storage option for avian influenza sampling in logistically challenging conditions.

    abstract：:Surveillance of wild birds is critical in monitoring for highly pathogenic avian influenza A viruses (AIVs). However, a successful surveillance regime requires proper treatment of samples in the field - rapid placement of samples in -80°C and subsequent maintenance of cold-chain. Given the logistical difficulties of t...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2017.11.004

    authors： Wille M,Yin H,Lundkvist Å,Xu J,Muradrasoli S,Järhult JD

    更新日期：2018-02-01 00:00:00

  • Human cytomegalovirus DNA kinetics using a novel HCMV DNA quantitative assay in white blood cells of immunocompromised patients under Ganciclovir therapy.

    abstract：:The clearance of human cytomegalovirus (HCMV) was evaluated in infected patients under Ganciclovir (GCV) treatment, using a novel HCMV DNA quantitation assay (HCMV DNA hybrid capture system, Murex Diagnostics). Peripheral white blood cells (WBC) from whole blood specimens of seven AIDS patients, three kidney and two a...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/s0166-0934(97)02180-0

    authors： Payan C,Veal N,Sarol L,Villarmé M,Ngohou C,Riberi P,François S,Ifrah N,Loison J,Chennebault JM,Pichard E,Kouyoumdjian S,Lunel F

    更新日期：1997-04-01 00:00:00

  • Construction of infectious cDNA clone derived from a classical swine fever virus field isolate in BAC vector using in vitro overlap extension PCR and recombination.

    abstract：:To develop reverse genetics system of RNA viruses, cloning of full-length viral genome is required which is often challenging due to many steps involved. In this study, we report cloning of full-length cDNA from an Indian field isolate (CSFV/IVRI/VB-131) of classical swine fever virus (CSFV) using in vitro overlap ext...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2015.10.006

    authors： Kamboj A,Saini M,Rajan LS,Patel CL,Chaturvedi VK,Gupta PK

    更新日期：2015-12-15 00:00:00

  • HIV-1 DNA vaccine efficacy is enhanced by coadministration with plasmid encoding IFN-alpha.

    abstract：:Numerous strategies have been employed in an attempt to improve the immunogenicity and efficacy of nucleic acid vaccines. In the present study, the immunogenicity in the induction of humoral and cellular immune responses to HIV-1 DNA vaccine expressing a chimeric gene of gag and gp120 and the adjuvant effect of IFN-al...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2007.07.016

    authors： Jiang W,Ren L,Jin N

    更新日期：2007-12-01 00:00:00

  • A real time RT-PCR assay for the specific detection of Peste des petits ruminants virus.

    abstract：:Peste des petits ruminants virus (PPRV) causes a devastating disease of small ruminants present across much of Africa and Asia. Recent surveillance activities and phylogenetic analyses have suggested that the virus is an emerging problem as it is now being detected in areas previously free of the disease. As such, the...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2010.11.022

    authors： Batten CA,Banyard AC,King DP,Henstock MR,Edwards L,Sanders A,Buczkowski H,Oura CC,Barrett T

    更新日期：2011-02-01 00:00:00

  • The impact of highly active antiretroviral therapy by the oral route on the CD8 subset in monkeys infected chronically with SHIV 89.6P.

    abstract：:The objective of this study was to assess the impact of highly active antiretroviral therapy (HAART) by an oral route on the peripheral blood CD8 subset in the monkeys infected persistently with a pathogenic strain, SHIV(89.6P). Two rhesus macaques were inoculated intravenously with SHIV(89.6P), then treated with the ...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/s0166-0934(03)00201-5

    authors： Yoshimura K,Ido E,Akiyama H,Kimura T,Aoki M,Suzuki H,Mitsuya H,Hayami M,Matsushita S

    更新日期：2003-09-01 00:00:00

  • Development and validation of a real-time RT-PCR assay for generic detection of pospiviroids.

    abstract：:In many countries phytosanitary regulations apply to Potato spindle tuber viroid, because it can cause serious diseases in potato and tomato crops. Other pospiviroids, some of which are distributed widely in ornamental crops, can cause similar diseases. Consequently, there is a need for a reliable and cost-effective g...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2012.09.004

    authors： Botermans M,van de Vossenberg BT,Verhoeven JT,Roenhorst JW,Hooftman M,Dekter R,Meekes ET

    更新日期：2013-01-01 00:00:00

  • A time-resolved fluoroimmunoassay for the quantitation of rabies virus nucleoprotein in the rabies vaccine.

    abstract：:Sensitive, precise and rapid detection tests are needed in the quality control of rabies vaccine for rabies virus nucleoprotein. Previous studies for quantitation of rabies virus nucleoprotein focused on enzyme-linked immunosorbent assay (ELISA). A novel immunoassay for rapid determination of rabies virus nucleoprotei...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2014.06.002

    authors： Lin G,Huang H,Liu T,He C,Liu J,Chen S,Hou J,Ren Z,Dong W,Wu Y

    更新日期：2014-09-01 00:00:00

  • Rapid molecular detection of Lujo virus RNA.

    abstract：:Lujo virus is an emerging arenavirus circulating in Southern Africa. Although to date there has only been a single outbreak of the novel haemorrhagic disease resulting from human infection with this virus, the case-fatality rate of exposed individuals, including nosocomial transmission, was 80%. The ability to identif...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2013.09.006

    authors： Atkinson B,Chamberlain J,Dowall SD,Cook N,Bruce C,Hewson R

    更新日期：2014-01-01 00:00:00

  • Competitive polymerase chain reaction using an internal standard: application to the quantitation of viral DNA.

    abstract：:A general strategy for the construction of an internal standard for the polymerase chain reaction (PCR) is described together with its application in the evaluation of clinical samples. This internal standard is a plasmid containing a modified target sequence that is co-amplified with the native target using the same ...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/0166-0934(92)90099-y

    authors： Telenti A,Imboden P,Germann D

    更新日期：1992-09-01 00:00:00

  • A novel approach to the detection of classical swine fever virus by RT-PCR with a fluorogenic probe (TaqMan).

    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

    authors： McGoldrick A,Lowings JP,Ibata G,Sands JJ,Belak S,Paton DJ

    更新日期：1998-06-01 00:00:00

  • Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design.

    abstract：:Allele-specific PCR based on subtype consensus sequences is a powerful technique for detecting low frequency drug resistant mutants in HIV-1 infected patients. However, this approach can be limited by genetic variation in the region complementary to the primers, leading to variability in allele detection. The goals of...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2009.11.025

    authors： Boltz VF,Maldarelli F,Martinson N,Morris L,McIntyre JA,Gray G,Hopley MJ,Kimura T,Mayers DL,Robinson P,Mellors JW,Coffin JM,Palmer SE

    更新日期：2010-03-01 00:00:00

  • Detection and quantitation of HBV DNA in miniaturized samples: multi centre study to evaluate the performance of the COBAS ® AmpliPrep/COBAS ® TaqMan ® hepatitis B virus (HBV) test v2.0 by the use of plasma or serum specimens.

    abstract：:Laboratory analysis of blood specimens is an increasingly important tool for rapid diagnosis and control of therapy. So, miniaturization of test systems is needed, but reduced specimens might impair test quality. For rapid detection and quantitation of HBV DNA, the COBAS(®) AmpliPrep/COBAS(®) TaqMan(®) HBV test has pr...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2010.07.025

    authors： Berger A,Gohl P,Stürmer M,Rabenau HF,Nauck M,Doerr HW

    更新日期：2010-11-01 00:00:00

  • Sensitive analytic ELISAs for subclass herpes virus IgG.

    abstract：:The subclass distribution of antiviral antibodies to three herpes viruses was studied in a population of healthy blood donors. Subclassification by monoclonal antibodies led to the identification of certain viral IgG patterns. IgG1 appeared to be formed in response to almost all CMV, HSV-1 and VZV infections. A higher...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/0166-0934(85)90061-8

    authors： Gilljam G,Sundqvist VA,Linde A,Pihlstedt P,Eklund AE,Wahren B

    更新日期：1985-03-01 00:00:00

  • Effects of codon-optimization on protein expression by the human herpesvirus 6 and 7 U51 open reading frame.

    abstract：:Codon-optimization refers to the alteration of gene sequences, to make codon usage match the available tRNA pool within the cell/species of interest. Codon-optimization has emerged as a powerful tool to increase protein expression by genes from small RNA and DNA viruses, which commonly contain overlapping reading fram...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/s0166-0934(03)00173-3

    authors： Bradel-Tretheway BG,Zhen Z,Dewhurst S

    更新日期：2003-08-01 00:00:00

  • Development of an immunochromatographic strip for rapid detection of antibodies against classical swine fever virus.

    abstract：:The genes encoding the Erns and E2 antigen epitopes of classical swine fever virus (CSFV) were expressed as a chimeric protein in Escherichia coli BL21 by pET expression system. The antigenicity of the expressed protein CnC2 was identified by indirect enzyme-linked immunoabsorbant assay (ELISA) and immunoblot with ant...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2011.12.006

    authors： Li X,Wang L,Shi X,Zhao D,Yang J,Yang S,Zhang G

    更新日期：2012-03-01 00:00:00

  • Development of a high-throughput human rhinovirus infectivity cell-based assay for identifying antiviral compounds.

    abstract：:Asthma and chronic obstructive pulmonary disease exacerbations are associated with human rhinovirus (HRV) lung infections for which there are no current effective antiviral therapies. To date, HRV infectivity of cells in vitro has been measured by a variety of biochemical and immunological methods. This paper describe...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2011.02.002

    authors： Phillips T,Jenkinson L,McCrae C,Thong B,Unitt J

    更新日期：2011-05-01 00:00:00

  • Ferrihydrite treatment to mitigate inhibition of RT-qPCR virus detection from large-volume environmental water samples.

    abstract：:Molecular assays are currently the most widely used method to quantify pathogenic viruses in water; however, their performance is often disrupted by matrices present in environmental samples. The present study used ferrihydrite (Fh) treatment to mitigate inhibition of RT-qPCR virus detection from environmental water c...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2018.10.018

    authors： Canh VD,Osawa H,Inoue K,Kasuga I,Takizawa S,Furumai H,Katayama H

    更新日期：2019-01-01 00:00:00

  • Duplex SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus and canine astrovirus.

    abstract：:A duplex SYBR Green I-based real-time PCR assay was established for the simultaneous detection of canine kobuvirus (CaKoV) and canine astrovirus (CaAstV). This assay can easily distinguish the two viruses according to their different melting temperatures (Tm) of 80 °C for CaKoV and 86.5 °C for CaAstV; other canine ent...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2021.114066

    authors： Wang Y,Li Y,Cui Y,Jiang S,Liu H,Wang J,Li Y

    更新日期：2021-01-13 00:00:00

  • Homogeneous sugar modification improves crystallization of measles virus hemagglutinin.

    abstract：:Measles virus (MV) enters cells by binding to the signaling lymphocyte activation molecule (also called CD150) on the cell surface, and thus shows the lymphotropism and immunosuppressive effects. The head domain (residues Asp149 to Arg617) of the MV hemagglutinin (MV-H), the attachment protein, was produced using a tr...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2008.01.008

    authors： Hashiguchi T,Kajikawa M,Maita N,Takeda M,Kuroki K,Sasaki K,Kohda D,Yanagi Y,Maenaka K

    更新日期：2008-04-01 00:00:00

  • Detection of minority variants within bovine respiratory syncytial virus populations using oligonucleotide-based microarrays.

    abstract：:Microarray technology, originally developed for highly parallel examination of gene expression is regarded as a potential tool in prognosis and diagnosis. With respect to a discrimination analysis, difference as small as one nucleotide base can be distinguished using oligonucleotide-based microarrays. However, this de...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2007.10.026

    authors： Leberre V,Baranowski E,Deplanche M,Trouilh L,François JM

    更新日期：2008-03-01 00:00:00

  • Comparison of multiple viral population characterization methods on a candidate cross-protection Citrus tristeza virus (CTV) source.

    abstract：:Citrus tristeza virus (CTV) is the most economically important virus found on citrus and influences production worldwide. The 3' half of the RNA genome is generally conserved amongst sources, whereas the 5' portion is more divergent, allowing for the classification of the virus into a number of genotypes based on sequ...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2016.09.003

    authors： Kleynhans J,Pietersen G

    更新日期：2016-11-01 00:00:00

  • Direct RT-PCR method for detecting two chrysanthemum viroids using minimal amounts of plant tissue.

    abstract：:A direct reverse transcription-polymerase chain reaction (RT-PCR) method for detecting the chrysanthemum stunt viroid (CSVd) and chrysanthemum chlorotic mottle viroid (CChMVd) to screen for a viroid-free chrysanthemum plant at a small plant size was established and named microtissue direct RT-PCR. A razor or syringe n...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2005.07.001

    authors： Hosokawa M,Matsushita Y,Uchida H,Yazawa S

    更新日期：2006-01-01 00:00:00

  • Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, 'definetherain'.

    abstract：:Droplet Digital PCR (ddPCR) represents a new and alternative platform to conventional quantitative-PCR (qPCR) for the quantitation of DNA templates. However, the proposed improvement in sensitivity and reproducibility offered by ddPCR is not yet fully proven, partly because the delineation between positive and negativ...

    journal_title：Journal of virological methods

    pub_type： 杂志文章

    doi：10.1016/j.jviromet.2014.02.020

    authors： Jones M,Williams J,Gärtner K,Phillips R,Hurst J,Frater J

    更新日期：2014-06-01 00:00:00