HCV genotyping should be performed in all HCV-infected
persons prior to treatment initiation in order to plan for the
duration of therapy and to estimate the likelihood of response.
An assay based on viral population sequencing, reverse
hybridization or real-time PCR, which has been validated for
correct subtyping of at least subtypes 1a and 1b should be used.
Two commercial assays are frequently used for HCV genotypes:
– TruGene™ HCV Genotyping kit (Siemens Healthcare
Diagnostics Division, Tarrytown, NY), based on direct
sequence analysis of the 5’ UTR (untranslated region),
– Versant™ HCV Genotype Assay LiPA (version I; Siemens
Medical Solutions, Diagnostics Division, Fernwald,
Germany), based on reverse hybridization analysis with
genotype-specific oligonucleotide probes binding to the
5’ UTR. A second generation line probe assay (LiPA) contains
probes targeting both the 5’ UTR and the core regions of the
viral genome, improving the accuracy of discrimination
between subtypes 1a and 1b.
A new test which uses real-time PCR technology for HCV
genotyping has recently been developed by Abbott Molecular.
HCV resistance monitoring. Like HIV and HBV, HCV has a high
replication rate and replicates via an error-prone mechanism,
generating resistance variants. In the near future, HCV
resistance testing (Kieffer 2010) will most probably be part of the
clinical monitoring algorithms. Assays based on viral population
sequencing require a minimum VL of 1000 IU/mL and define the
most common mutation patterns, without detecting the lowfrequency
variants. Accurate determination of viral
genotype/subtype is critical for resistance testing during the
development of new direct-acting antivirals (DAAs) (Chevaliez
2009).
Pretreatment samples are analyzed to detect known or novel
predominant viral polymorphisms and to provide the
Patients’ monitoring during and after treatment | 35
comparator for mutations emerging at later time points, during
or after treatment. On-treatment viremic samples are analyzed
to determine specific changes associated with decreased
susceptibility and virologic failure. Post-treatment samples are
analyzed for persistence or loss of resistant variants and may
help distinguish between re-infection and relapse. More details
on the impact of resistance on HCV treatment are given in
chapter 4.
persons prior to treatment initiation in order to plan for the
duration of therapy and to estimate the likelihood of response.
An assay based on viral population sequencing, reverse
hybridization or real-time PCR, which has been validated for
correct subtyping of at least subtypes 1a and 1b should be used.
Two commercial assays are frequently used for HCV genotypes:
– TruGene™ HCV Genotyping kit (Siemens Healthcare
Diagnostics Division, Tarrytown, NY), based on direct
sequence analysis of the 5’ UTR (untranslated region),
– Versant™ HCV Genotype Assay LiPA (version I; Siemens
Medical Solutions, Diagnostics Division, Fernwald,
Germany), based on reverse hybridization analysis with
genotype-specific oligonucleotide probes binding to the
5’ UTR. A second generation line probe assay (LiPA) contains
probes targeting both the 5’ UTR and the core regions of the
viral genome, improving the accuracy of discrimination
between subtypes 1a and 1b.
A new test which uses real-time PCR technology for HCV
genotyping has recently been developed by Abbott Molecular.
HCV resistance monitoring. Like HIV and HBV, HCV has a high
replication rate and replicates via an error-prone mechanism,
generating resistance variants. In the near future, HCV
resistance testing (Kieffer 2010) will most probably be part of the
clinical monitoring algorithms. Assays based on viral population
sequencing require a minimum VL of 1000 IU/mL and define the
most common mutation patterns, without detecting the lowfrequency
variants. Accurate determination of viral
genotype/subtype is critical for resistance testing during the
development of new direct-acting antivirals (DAAs) (Chevaliez
2009).
Pretreatment samples are analyzed to detect known or novel
predominant viral polymorphisms and to provide the
Patients’ monitoring during and after treatment | 35
comparator for mutations emerging at later time points, during
or after treatment. On-treatment viremic samples are analyzed
to determine specific changes associated with decreased
susceptibility and virologic failure. Post-treatment samples are
analyzed for persistence or loss of resistant variants and may
help distinguish between re-infection and relapse. More details
on the impact of resistance on HCV treatment are given in
chapter 4.
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