Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pmed.1000031
Title: A novel diagnostic target in the hepatitis C virus genome
Authors: Drexler J.F.
Kupfer B.
Petersen N.
Grotto R.M.T.
Rodrigues S.M.C.
Grywna K.
Panning M.
Annan A.
Silva G.F.
Douglas J.
Koay E.C. 
Smuts H.
Netto E.M.
Simmonds P.
De Moura Campos Pardini M.I.
Roth W.K.
Drosten C.
Keywords: article
blood donor
blood sampling
Brazil
controlled study
cost benefit analysis
gene sequence
genotype
Germany
Hepatitis C virus
human
nucleic acid amplification
nucleotide sequence
screening test
Singapore
South Africa
turnaround time
United Kingdom
virus detection
virus genome
virus load
5' untranslated region
blood
genetics
hepatitis C
isolation and purification
methodology
molecular genetics
virology
virus load
virus RNA
5' Untranslated Regions
Base Sequence
Genome, Viral
Genotype
Hepacivirus
Hepatitis C
Humans
Molecular Sequence Data
RNA, Viral
Viral Load
Issue Date: 2009
Citation: Drexler J.F., Kupfer B., Petersen N., Grotto R.M.T., Rodrigues S.M.C., Grywna K., Panning M., Annan A., Silva G.F., Douglas J., Koay E.C., Smuts H., Netto E.M., Simmonds P., De Moura Campos Pardini M.I., Roth W.K., Drosten C. (2009). A novel diagnostic target in the hepatitis C virus genome. PLoS Medicine 6 (2) : 210-220. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pmed.1000031
Rights: Attribution 4.0 International
Abstract: Background Detection and quantification of hepatitis C virus (HCV) RNA is integral to diagnostic and therapeutic regimens. All molecular assays target the viral 5?-noncoding region (5?-NCR), and all show genotype-dependent variation of sensitivities and viral load results. Non-western HCV genotypes have been under-represented in evaluation studies. An alternative diagnostic target region within the HCV genome could facilitate a new generation of assays. Methods and Findings In this study we determined by de novo sequencing that the 3?-X-tail element, characterized significantly later than the rest of the genome, is highly conserved across genotypes. To prove its clinical utility as a molecular diagnostic target, a prototype qualitative and quantitative test was developed and evaluated multicentrically on a large and complete panel of 725 clinical plasma samples, covering HCV genotypes 1-6, from four continents (Germany, UK, Brazil, South Africa, Singapore). To our knowledge, this is the most diversified and comprehensive panel of clinical and genotype specimens used in HCV nucleic acid testing (NAT) validation to date. The lower limit of detection (LOD) was 18.4 IU/ml (95% confidence interval, 15.3-24.1 IU/ml), suggesting applicability in donor blood screening. The upper LOD exceeded 10-9 IU/ml, facilitating viral load monitoring within a wide dynamic range. In 598 genotyped samples, quantified by Bayer VERSANT 3.0 branched DNA (bDNA), X-tail-based viral loads were highly concordant with bDNA for all genotypes. Correlation coefficients between bDNA and X-tail NAT, for genotypes 1-6, were: 0.92, 0.85, 0.95, 0.91, 0.95, and 0.96, respectively; X-tail-based viral loads deviated by more than 0.5 log10 from 5?-NCR-based viral loads in only 12% of samples (maximum deviation, 0.85 log10). The successful introduction of X-tail NAT in a Brazilian laboratory confirmed the practical stability and robustness of the X-tail-based protocol. The assay was implemented at low reaction costs (US$8.70 per sample), short turnover times (2.5 h for up to 96 samples), and without technical difficulties. Conclusion This study indicates a way to fundamentally improve HCV viral load monitoring and infection screening. Our prototype assay can serve as a template for a new generation of viral load assays. Additionally, to our knowledge this study provides the first open protocol to permit industry-grade HCV detection and quantification in resource-limited settings.
Source Title: PLoS Medicine
URI: https://scholarbank.nus.edu.sg/handle/10635/161678
ISSN: 15491277
DOI: 10.1371/journal.pmed.1000031
Rights: Attribution 4.0 International
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