Hepatitis Virus Characterisation
HAV RNA Assays
HAV PCR is used for the qualitative detection of HAV RNA in blood. All positive isolates are sequenced using an international primer set and compared to other sequences in our extensive database to determine potential sources of infection.
HBV Quantification (viral load) Assay
This test measures the amount of HBV present in the blood and is used to guide clinical decisions and monitor response to therapy. The platforms used at VIDRL are the Abbott Alinity m, the Roche COBAS 6800 and the Cepheid GeneXpert assays, which have a dynamic range of 10 – 1,000,000,000 IU/mL.
Sequencing of the HBV polymerase/reverse transcriptase region is performed to determine genotype and drug resistance mutations (including the YMDD motif). This sequence also covers the overlapping surface region to detect vaccine and immune escape mutants.
VIDRL also performs sequencing of the HBV basal core promoter (BCP) and pre-core (PC) regions to detect mutations associated with reduced or abrogated HBeAg synthesis.
HCV RNA Qualitative Assay
HCV PCR is used for the qualitative detection of HCV RNA in blood. The commercial platforms used at VIDRL include the Abbott Alinity m and the Roche 6800. The limit of detection for the Abbott and Roche assays are 12 and 15 International Units (IU)/mL respectively.
HCV Quantification (viral load) Assay
This test measures the amount of HCV RNA present in the blood and is also a useful predictor of response to therapy. The platform used at VIDRL is the Abbott Alinity m assay which has a dynamic range of 12 – 100,000,000 IU/mL.
HCV Genotype Assay
HCV is an RNA virus with considerable heterogeneity. Using sequence analysis and phylogenetics, HCV can be classified into distinct genotypes which, in some instances, can be further divided into subtypes. Determination of HCV genotype may be a clinically useful tool as it plays a role in treatment outcome. However, with the implementation of pan-genotypic direct acting antivirals, genotyping does not have to be performed prior to commencing therapy. At VIDRL, genotyping is performed using either the Abbott RealTime HCV Genotype II assay, the Versant HCV Genotype 2.0 assay LiPA II assay, or by sequence analysis of the core region of the genome.
HCV Resistance Associated Variants
Direct-acting antivirals have recently been developed to treat chronic HCV infection, and have substantially increased sustained viral response rates. Nevertheless, pre-existing resistance associated substitutions (RAS) can reduce the efficacy of these new treatments. In addition, such RAS, which are normally found as a minor quasispecies, can be selected on treatment to become predominant also reducing drug efficacy. VIDRL performs population-based sequencing to determine RAS to NS5A inhibitors.
HDV Quantification (viral load) Assay
This test measures the amount of HDV RNA present in the blood and is used to determine current infection and monitor response to therapy. VIDRL uses an in-house assay that detects all known genotypes.
HEV Quantification (viral load) Assays
HEV viral load testing is performed for the quantification of HEV RNA in blood. All positive isolates are sequenced using an international primer set and compared to other sequences in our extensive database to provide potential sources of infection.