A novel diagnostic target in the hepatitis C virus genome.
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.


RESULTS
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.


CONCLUSIONS
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.
Drexler
Jan Felix
JF
Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
Kupfer
Bernd
B
Petersen
Nadine
N
Grotto
Rejane Maria Tommasini
RM
Rodrigues
Silvia Maria Corvino
SM
Grywna
Klaus
K
Panning
Marcus
M
Annan
Augustina
A
Silva
Giovanni Faria
GF
Douglas
Jill
J
Koay
Evelyn S C
ES
Smuts
Heidi
H
Netto
Eduardo M
EM
Simmonds
Peter
P
Pardini
Maria Inês de Moura Campos
MI
Roth
W Kurt
WK
Drosten
Christian
C
D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D016679:Genome, Viral / Q000235:genetics; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics / Q000302:isolation & purification*; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000097:blood* / Q000235:genetics; D019562:Viral Load / Q000379:methods*
D020121:5' Untranslated Regions; D012367:RNA, Viral