A multicenter evaluation of the Abbott RealTime HCV Genotype II assay

Ciotti, Marco; Marcuccilli, Fabbio; Guenci, Tania; Babakir‐Mina, Muhammed; Chiodo, F; Favarato, M.; Perno, Carlo Federico

doi:10.1016/j.jviromet.2010.03.017

Cited by 30 publications

(23 citation statements)

References 12 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%

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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%

“…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.…”

mentioning

confidence: 99%

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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“…Both commercial assays, the LiPA 2.0 and the Realtime II, have been widely used and reported to yield consistent results (23). However, few samples identified as genotype 6 were included in these previous studies.…”

Section: Discussionmentioning

confidence: 99%

“…Generally, the 5= untranslated region (UTR) is the target for genotyping. Although this region is highly conserved, a well-characterized set of polymorphisms predicting the HCV genotype can be detected by restriction fragment length polymorphism (18), probe hybridization (19)(20)(21)(22), genotype-specific real-time PCR (23,24), or Sanger and next-generation sequencing (25)(26)(27)(28)(29). The determination of HCV genotype 6, however, seems more challenging due to the sequence diversity and similarity to that of genotype 1.…”

Section: H Epatitis C Virus (Hcv) Infects 170 Million People Worldwidementioning

confidence: 99%

“…Thus, this method saves time and labor and is resistant to potential PCR aerosol contamination compared to other assays. In a recent study, the LiPA 2.0 and Realtime II assay were shown to yield consistent HCV genotyping results (23). Their abilities to identify genotype 6, however, have not been well studied due to the limited number of genotype 6 samples available.…”

Section: H Epatitis C Virus (Hcv) Infects 170 Million People Worldwidementioning

confidence: 99%

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Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6

Yang

et al. 2014

J Clin Microbiol

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The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5= untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1.

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Indeterminate genotypes of hepatitis C virus by the Abbott RealTime HCV Genotype II assay in Morocco. About eight cases resolved by a sequencing method

Mesbahi

Kabbaj

Malki

et al. 2018

Journal of Medical Virology

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The early detection and genotyping of the hepatitis C virus (HCV) are important in the management of this infection. The genotype is the major factor influencing treatment decisions. That's why it is necessary to use fast and accurate methods in its determination. This study reports, over a period of 3 years (from May 2012 to July 2015), the percentage of indeterminate genotypes by the Abbott RealTime HCV Genotype II test and their results using a sequencing technique. Of 309 samples of 309 patients tested, 11 were indeterminate (4.4%). There were three cases of cross-reactivity (1b/4 in one case, 2/5 in two cases) and a possible co-infection 1 + 4. Among those indeterminate genotypes, cross-reactivities and co-infections, ten samples were tested by sequencing. The results were for four of them a 1d subtype, five were a 2i subtype and one was a 2l subtype. These results support the thesis of complementarity between the two methods: genotyping for the detection of mixed reactions and sequencing for resolving indeterminate cases by genotyping.

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A multicenter evaluation of the Abbott RealTime HCV Genotype II assay

Cited by 30 publications

References 12 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

Performance Comparison of the Versant HCV Genotype 2.0 Assay (LiPA) and the Abbott Realtime HCV Genotype II Assay for Detecting Hepatitis C Virus Genotype 6

Indeterminate genotypes of hepatitis C virus by the Abbott RealTime HCV Genotype II assay in Morocco. About eight cases resolved by a sequencing method

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