Evaluation of a New-Generation Line-Probe Assay That Detects 5' Untranslated and Core Regions to Genotype and Subtype Hepatitis C Virus

Nadarajah, Rohan; Khan, Gulfaraz; Miller, Steven A.; Brooks, Geo. F.

doi:10.1309/rbaac0hjfwrjb1hd

Cited by 18 publications

(11 citation statements)

References 12 publications

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“…Genotyping was performed by reverse hybridization, and viruses were not sequenced; misclassification could have occurred [43]. Patients may also be infected with multiple GTs, especially IDU who have frequent opportunities for exposure [44], and the assay would have only identified the dominant virus [45].…”

Section: Discussionmentioning

confidence: 99%

Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California

et al. 2011

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BackgroundHepatitis C virus (HCV) genotype (GT) has become an important measure in the diagnosis and monitoring of HCV infection treatment. In the United States (U.S.) HCV GT 1 is reported as the most common infecting GT among chronically infected patients. In Europe, however, recent studies have suggested that the epidemiology of HCV GTs is changing.MethodsWe assessed HCV GT distribution in 460 patients from three HCV-infected high risk populations in San Francisco, and examined patterns by birth cohort to assess temporal trends. Multiple logistic regression was used to assess factors independently associated with GT 1 infection compared to other GTs (2, 3, and 4).ResultsOverall, GT 1 was predominant (72.4%), however younger injection drug users (IDU) had a lower proportion of GT 1 infections (54.7%) compared to older IDU and HIV-infected patients (80.5% and 76.6%, respectively). Analysis by birth cohort showed increasing proportions of non-GT 1 infections associated with year of birth: birth before 1970 was independently associated with higher adjusted odds of GT 1: AOR 2.03 (95% CI: 1.23, 3.34). African-Americans as compared to whites also had higher adjusted odds of GT 1 infection (AOR: 3.37; 95% CI: 1.89, 5.99).ConclusionsAlthough, HCV GT 1 remains the most prevalent GT, especially among older groups, changes in GT distribution could have significant implications for how HCV might be controlled on a population level and treated on an individual level.

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Section: Discussionmentioning

confidence: 99%

Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California

et al. 2011

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“…While with version 1 of the line probe assay HCV subtypes 1a and 1b were correctly identified in only Ͻ90% of the patient samples, a Ͼ95% accuracy for correct subtyping is achievable with version 2 (1,4,6). In addition, version 2 correctly identifies samples harboring genotype 6 (4,20). HCV RNA assays.…”

Section: Methodsmentioning

confidence: 99%

Differences between Two Real-Time PCR-Based Hepatitis C Virus (HCV) Assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and One Signal Amplification Assay (Versant HCV RNA 3.0) for RNA Detection and Quantification

et al. 2008

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Hepatitis C virus (HCV) RNA detection and quantification are the key diagnostic tools for the management of hepatitis C. Commercially available HCV RNA assays are calibrated to the HCV genotype 1 (gt1)-based WHO standard. Significant differences between assays have been reported. However, it is unknown which assay matches the WHO standard best, and little is known about the sensitivity and linear quantification of the assays for non-gt1 specimens. Two real-time reverse transcriptase PCR-based assays (RealTime HCV and Cobas Ampliprep/Cobas TaqMan HCV [CAP/CTM]) and one signal amplification-based assay (the Versant HCV RNA, version 3.0, branched DNA [bDNA] assay) were compared for their abilities to quantify HCV RNA in clinical specimens (n ‫؍‬ 65) harboring HCV isolates of gt1 to g5. The mean differences in the amounts detected by RealTime HCV in comparison to those detected by the bDNA assay and CAP/CTM were ؊0.02 and 0.72 log 10 IU/ml HCV RNA, respectively, for gt1; ؊0.22 and 0.03 log 10 IU/ml HCV RNA, respectively, for gt2; ؊0.27 and ؊0.22 log 10 IU/ml HCV RNA, respectively, for gt3; ؊0.19 and ؊1.27 log 10 IU/ml HCV RNA, respectively, for gt4; and ؊0.03 and 0.09 log 10 IU/ml HCV RNA, respectively, for gt5. The lower limits of detection for RealTime HCV and CAP/CTM were 16.8 and 10.3 IU/ml, respectively, for the WHO standard and in the range of 4.7 to 9.0 and 3.4 to 44.4 IU/ml, respectively, for clinical specimens harboring gt1 to gt6. Direct comparison of the two assays with samples of the WHO standard (code 96/798) with high titers yielded slightly smaller amounts by RealTime HCV (؊0.2 log 10 at 1,500 IU/ml and ؊0.3 log 10 at 25,000 IU/ml) and larger amounts by CAP/CTM (0.3 log 10 at 1,500 IU/ml and 0.2 log 10 at 25,000 IU/ml). Finally, all three tests were linear between 4.0 ؋ 10 3 and 1.0 ؋ 10 6 IU/ml (correlation coefficient, >0.99). In conclusion, the real-time PCR based assays sensitively detected all genotypes and showed comparable linearities for the quantification of HCV RNA, with the exception of gt1 and gt4. The previously reported differences in the absolute quantification of samples harboring gt1 were confirmed and may be explained by different calibrations to the WHO standard.Hepatitis C virus (HCV) infection is a common cause of chronic liver disease that can lead to end-stage liver disease, including hepatocellular carcinoma.At present, combination therapy with pegylated interferon and ribavirin is the standard of care. However, this treatment regimen appears to be effective in only 40% to 50% of patients infected with genotype 1 and approximately 80% of patients infected with genotypes 2 and 3 (12, 13, 16).A sustained virologic response, defined as undetectable HCV RNA at least 6 months after the completion of therapy, may be predicted by a number of host and viral factors, including age, race, liver fibrosis, the HCV genotype, and the baseline viral load.Recent reports suggest that decisions on the optimal treatment duration may be made on the basis of the baseline viral load and the virologi...

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“…Indeterminate results (of genotypes 1, 2, 4, and 6) have also been reported for this assay, with percentages ranging between 0% and 4.5%. 9,[14][15][16][17][18] Similarly, the Versant assay also fails to identify the HCV-1 subtype in 2.2-7.4% of the cases. 9,11,16,18 In our hands, an indeterminate result was obtained in two HCV-1 infections (0.96%, N = 209), and the HCV-1 subtype was not assigned in 2 of 118 (1.7%) cases.…”

Section: Introductionmentioning

confidence: 99%

Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice

González

Gomes-Fernandes

Bascuñana

et al. 2013

Journal of Clinical Virology

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Evaluation of a New-Generation Line-Probe Assay That Detects 5' Untranslated and Core Regions to Genotype and Subtype Hepatitis C Virus

Cited by 18 publications

References 12 publications

Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California

Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California

Differences between Two Real-Time PCR-Based Hepatitis C Virus (HCV) Assays (RealTime HCV and Cobas AmpliPrep/Cobas TaqMan) and One Signal Amplification Assay (Versant HCV RNA 3.0) for RNA Detection and Quantification

Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice

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