Medizinische Universität Graz Austria/Österreich - Forschungsportal - Medical University of Graz
Gewählte Publikation:
Handler, V.
Detection of recombinant hepatitis C virus strains
Humanmedizin; [ Diplomarbeit ] Graz Medical University; 2018. pp.
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- Autor*innen der Med Uni Graz:
- Betreuer*innen:
- Kessler Harald
- Stelzl Evelyn
- Altmetrics:
- Abstract:
- Background: According to the most recent EASL recommendations (European Association for the Study of the Liver) on the management of hepatitis C virus (HCV) infection, HCV genotypes and genotype 1 subtypes (1a or 1b) should be assessed prior to treatment initiation, as this will impact the choice and duration of direct-antiviral treatment regimens. Currently, HCV is classified into 7 different genotypes and 67 subtypes. Additionally, several natural intra- and intergenotypic recombinants of HCV have been identified. Among these, the so-called “St Petersburg variant”, a genotype 2k/1b recombinant, is the most prevalent worldwide. Objectives: To compare results obtained by assays using different molecular techniques for determination of HCV genotypes 1 and 2 as well as recombinant forms between these two genotypes. Materials and methods: In this study, 279 samples derived from patients with chronic HCV infection were investigated. HCV genotypes and subtypes were determined by the reverse hybridization-based VERSANT® HCV Genotype 2.0 assay (LiPA; Siemens Healthcare) that targets the 5´UTR and HCV core regions, and the real-time PCR based cobas® HCV GT (cobas; Roche Molecular Systems) assay that targets the 5´UTR, core, and NS5B regions. Assay results were compared to direct sequencing of the HCV core, NS2/NS3 junction, NS3, NS5A, and the NS5B regions as the reference standard. Results: In total, 53 patients had subtype 1b, 177 patients had genotype 2, and 48 patients had genotype 2/genotype 1 recombinants according to direct sequencing (2k/1b, n=46; 2b/1a, n=1; 2a/1b, n=1). Finally, one patient had a mixed genotype 1b + genotype 2b infection. All 53 samples with subtype 1b were correctly subtyped by the VERSANT® HCV Genotype 2.0 assay, and 51/53 samples were subtyped with the cobas® HCV GT, respectively (two samples yielded genotype 1 results only). Among genotype 2 samples, 177/177 and 174/177 samples were correctly reported as genotype 2 by the VERSANT® HCV Genotype 2.0 assay and the cobas® HCV GT, respectively (three samples yielded invalid results with the cobas® HCV GT). The VERSANT® HCV Genotype 2.0 assay reported all 48 genotype 2/genotype 1 recombinants as genotype 2, whereas the cobas® HCV GT assay reported 43 as genotype 1b/genotype 2 (which cannot rule out double infection) and five samples were reported as genotype 2 only. One sample was classified as mixed genotype 1+ genotype 2 infection when results obtained by all assays were taken into consideration. Conclusions: When analyzing HCV patient samples containing strains without recombination, analysis of the 5´UTR and core regions is sufficient, while identification of HCV recombinant forms requires inclusion of an additional region close to the 3´ end of the HCV genome.