Analysis of the 5′ Noncoding Region versus the NS5b Region in Genotyping Hepatitis C Virus Isolates from Blood Donors in France

Cantaloube, Jean-François; Laperche, Syria; Gallian, Pierre; Bouchardeau, Françoise; Lamballerie, Xavier de; Micco, Philippe de

doi:10.1128/jcm.02463-05

Cited by 61 publications

(70 citation statements)

References 42 publications

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“…It is possible that the sequences containing the polymorphisms in the 5= UTR that are responsible for subtype 1a/1b errors include variants in the NS5B gene that allow for correct subtype designation, while such variants are not present in the 5= UTR and the core gene. The genotype and subtype CRs of Abbott-RT-HCV are in agreement with previous reports (4,6,12). Using Abbott-RT-HCV for HCV-1 typing and subtyping, one sample with a light viral load (744 IU/ml) showed an indeterminate result, which is in line with the package insert instruction that the detection limit with a sample preparation of 0.5 ml is 500 IU/ml (13).…”

supporting

confidence: 91%

“…Using Abbott-RT-HCV for HCV-1 typing and subtyping, one sample with a light viral load (744 IU/ml) showed an indeterminate result, which is in line with the package insert instruction that the detection limit with a sample preparation of 0.5 ml is 500 IU/ml (13). Although the major (4,720,33,000, 36,000, and 62,000 IU/ml), three of which were correctly diagnosed by V-LiPA-2. Furthermore, another 15 HCV-1 samples with baseline viral loads of Ͻ100,000 (range, 6,080 to 84,800) IU/ml were correctly subtyped by Abbott-RT-HCV.…”

supporting

confidence: 69%

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Comparison of Abbott RealTime HCV Genotype II with Versant Line Probe Assay 2.0 for Hepatitis C Virus Genotyping

Liu¹,

Liang

Liu³

et al. 2015

J Clin Microbiol

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I n this retrospective hepatitis C virus (HCV) study (which has been registered at ClinicalTrials.gov under registration no. NCT00979979.), the Versant LiPA HCV 2.0 (V-LiPA-2) (1-5), the Abbott RealTime HCV GT II assay (Abbott-RT-HCV) (6, 7), and sequencing of the 5= untranslated region (UTR) and NS5B genes were used to genotype 225 samples from patients with HCV monoinfection and HCV-HBV or HCV-HIV dual infection.Reverse transcription, PCR amplification, and sequencing were performed with the ABI BigDye Terminator kit (see Table S1 in the supplemental material), and the samples were analyzed with the ABI 7900HT sequence detection system (Applied Biosystems, Life Technologies Corporation, Grand Island, NY). Sequence analysis was done with Seqscape, and genotypes were assigned by referring to GenBank and then subsequently confirmed by comparing the data with the Los Alamos database and by the generation of a phylogenetic tree by using the Phylogeny Inference Package (8). The V-LiPA-2 assay (Siemens Healthcare Diagnostics) was performed according to the manufacturer's instructions (2). The Abbott m2000sp system, which uses magnetic microparticles and automated sample preparation, was employed (9). Overall, the limit of detection is 500 IU/ml for Abbott-RT-HCV and 1,100 IU/ml for V-LiPA-2. The sensitivity of direct sequencing varies between laboratories. The cost of using Abbott-RT-HCV is about 42% less than that of using V-LiPA-2, and the time required to complete detection with Abbott-RT-HCV is also shorter than when either V-LiPA-2 or direct sequencing is used (Table 1).One hundred seventy-three males (67.8%) and 82 females (32.2%), with a median age of 51 (range, 20 to 79) years, were recruited. The median aspartate aminotransferase level was 76 (range, 18 to 448) IU/liter, and the median alanine aminotransferase level was 133 (range, 14 to 783) IU/liter. The mean HCV load was 6.59 (median, 5.99; range, 2.87 to 7.81) log 10 IU/ml.The V-LiPA-2 had a concordance rate (CR) of 99.2% for genotyping and 96.1% for subtyping. The CRs for genotypes 1, 2, 3, and 6 were Ͼ90%, and the CRs for subtypes 1a/1b, 2a/2b/2c, 3a, and 6a/6b were all Ͼ96% (Table 2). V-LiPA-2 misinterpreted five HCV-1 patients (one 1a as 1b, one 1aϩ1b as 1b, and three 1b as 1a). Two patients with subtype 2aϩ2c were misinterpreted as 2a, and one subtype 2b was misinterpreted as 1b by direct sequencing. V-LiPA-2 misinterpreted one subtype 6a as subtype 1b.The Abbott-RT-HCV had a CR of 99.6% for genotyping, and the CRs for genotypes 1, 2, 3, and 6 were Ͼ99% and that for subtype 1a/1b was 96.1% (Table 2). One case of discordance was a subtype 1b specimen with a light viral load (744 IU/ml), which could not be typed by Abbott-RT-HCV but was accurately subtyped as 1b by V-LiPA-2. One patient with a mixed subtype 1aϩ1b infection (viral load, 62,000 IU/ml) was interpreted as genotype 1 by Abbott-RT-HCV and as subtype 1b by V-LiPA-2. Two patients infected with subtype 1b (viral loads, 4,720 and 33,000 IU/ml) could not be subtyped by Abbott-RT-HCV but were be ...

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supporting

confidence: 91%

supporting

confidence: 69%

Comparison of Abbott RealTime HCV Genotype II with Versant Line Probe Assay 2.0 for Hepatitis C Virus Genotyping

Liu¹,

Liang

Liu³

et al. 2015

J Clin Microbiol

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“…111 These methods are used in epidemiologic studies 113 and have been implemented in the form of LDTs, which are offered for clinical diagnostic purposes by reference laboratories. An example is the HCV DupliType assay offered by Quest Diagnostics (New York, NY).…”

Section: Direct Sequencingmentioning

confidence: 99%

Diagnosis and Management of Hepatitis C Virus Infection

et al. 2015

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The hepatitis C virus (HCV) infects more than 200 million people globally, with increasing incidence, especially in developing countries. HCV infection frequently progresses to chronic liver disease, creating a heavy economic burden on resourcepoor countries and lowering patient quality of life. Effective HCV diagnosis, treatment selection, and treatment monitoring are important in stopping disease progression. Serological assays, which detect anti-HCV antibodies in the patient after seroconversion, are used for initial HCV diagnosis. Qualitative and quantitative molecular assays are used to confirm initial diagnosis, determine viral load, and genotype the dominant strain. Viral load and genotype information are used to guide appropriate treatment. Various other biomarker assays are performed to assess liver function and enable disease staging. Most of these diagnostic methods are mature and routinely used in high-resource countries with well-developed laboratory infrastructure. Few technologies, however, are available that address the needs of low-resource areas with high HCV prevalence, such as Africa and Southeast Asia.

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“…To compensate for these failures, alternative genomic regions have been proposed for the genotyping (7,11,21,28,35,44). Recently, a new version (Versant HCV Genotype 2.0; Bayer Health Care, Eragny, France) of a currently commer-cially available genotyping assay (Versant HCV Genotype assay; Bayer Health Care) based on the reverse hybridization of a 5ЈUTR segment (42) has been developed by the addition of Core sequence information, in order to improve the accuracy of HCV subtype classification for genotypes 1 and 6.…”

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confidence: 99%

Improvement of Hepatitis C Virus (HCV) Genotype Determination with the New Version of the INNO-LiPA HCV Assay

et al. 2007

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Hepatitis C virus (HCV) isolates have been classified into six main genotypes. Genotyping methods, and especially the widely used line probe assay (LiPA), are frequently based on the 5-untranslated region (5UTR). However, this region is not appropriate for discriminating HCV strains at the subtype level and for distinguishing many genotype 6 samples from genotype 1. We investigated the capacity of a novel LiPA (Versant HCV Genotype 2.0 assay) based on the simultaneous detection of 5UTR and Core regions for genotypes 1 and 6 to provide correct HCV genotypes (characterized with a phylogenetic analysis) in a set of HCV strains mainly encountered in Western countries. The improvement was assessed by comparing the results to those obtained with the previous version of the assay. Of the 135 tested samples, 64.7% were concordant for genotype group and subtype with sequencing reference results using the Versant HCV Genotype 2.0 assay versus 37.5% with the previous version. The yield was mainly related to a better characterization of genotype 1, since the accuracy, tested in 62 genotype 1 samples, increased from 45.2% with the first version to 96.8% with the new one. However, this new version necessitates a specific PCR and could no longer be used after 5UTR PCR used for current HCV infection diagnosis. Moreover, the information provided by 5UTR hybridization is not reliable for correctly identifying the diversity within genotypes 2 and 4. Thus, the Versant HCV Genotype 2.0 assay remains a useful tool for clinical practice when only the discrimination between major HCV genotypes is necessary.

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Analysis of the 5′ Noncoding Region versus the NS5b Region in Genotyping Hepatitis C Virus Isolates from Blood Donors in France

Cited by 61 publications

References 42 publications

Comparison of Abbott RealTime HCV Genotype II with Versant Line Probe Assay 2.0 for Hepatitis C Virus Genotyping

Comparison of Abbott RealTime HCV Genotype II with Versant Line Probe Assay 2.0 for Hepatitis C Virus Genotyping

Diagnosis and Management of Hepatitis C Virus Infection

Improvement of Hepatitis C Virus (HCV) Genotype Determination with the New Version of the INNO-LiPA HCV Assay

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