HCV Genotyping
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Further information
Scope of the tests
The treatment of hepatitis C virus (HCV) infection with antiviral drugs will vary depending on the genotype of the virus [de Bruijne et. al 2008]. Determination of genotype is made by sequencing of one or more of the variable genes of HCV, most commonly NS5b [Simmonds et al. 2005]. Currently, the Molecular Diagnostics Unit (MDU) routinely offers sequencing of the NS5b gene of HCV isolated from plasma. Samples with any viral load greater than 50 HIV DNA copies/ml plasma can be analysed, although increased assay failure rates are seen with low-load samples.
Test details (top of page)
The routine test generates a sequence covering 212 codons (636 bases) of the NS5b gene. The method is a fully validated in-house method. A summary of the validation is available from the Unit Manager.
Results reporting (top of page)
The raw data produced by the resistance assay is an edited nucleotide sequence. To generate a usable report this sequence is submitted to an on-line algorithm – the “Oxford HCV subtyping tool” (http://jose.med.kuleuven.be/genotypetool/html/). The interpretation is pasted into the final MDU report. If the user requires the sequence file (“FASTA” file) or the raw data chromatograms these can be supplied by arrangement with the Unit Manager.
Turnaround time (top of page)
We aim to issue reports within two weeks of receiving a sample. However, as we offer a bespoke service and make rigorous efforts to produce a result from any sample, submitted turnaround times may be extended if repeat testing is required.
Complaints (top of page)
If you are unhappy with the service provided by MDU or if you wish to make suggestions on how our service can be improved, please contact the Unit Manager.
References (top of page)
de Bruijne J, Buster EH, Gelderblom HC, Brouwer JT, de Knegt RJ, van Erpecum KJ, Schalm SW, Bakker CM, Zaaijer HL, Janssen HL, Reesink HW; Netherlands Association of Gastroenterologists and Hepatologists. Treatment of chronic hepatitis C virus infection – Dutch national guidelines. Neth J Med. 2008; 66: 311-22.
Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S et al. Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes. Hepatology 2005; 42: 962-973
