Abstract
Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5’NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with “not detected” results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. “Not detected” results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
Highlights
Chronic infection with hepatitis C virus (HCV) can progress to liver cirrhosis, hepatocellular cancer and death[1]
The reference method based on the NS5B and core sequencing and phylogenetic analysis was used for HCV classification
Among the samples with genotype 1 results without subtype assigned by GT II, the proportion of HCV subtype 1b isolates identified by sequencing or LiPA that could not be subtyped by the Genotype Plus RUO (GT Plus) assay was 9.6% (13/135) but varied geographically: 22.5% (9/40) in North-eastern Spain, 4.1% (2/49) in Southern Spain, and 4.3% (2/46) in Israel
Summary
Chronic infection with hepatitis C virus (HCV) can progress to liver cirrhosis, hepatocellular cancer and death[1]. While commercial genotyping assays use sub-genomic regions such as core or NS5B in addition to the more conserved 5′ untranslated (5′NC) region, the high genetic variability and small differences between genotypes and subtypes still remain a challenge for both real-time PCR and line probe-based HCV genotyping assays. This applies to HCV-1 subtyping[11,12,13,14,15,16,17,18,19,20,21]. The procedure is considered impractical for most clinical laboratories because it is time-consuming, less sensitive[21], may be technically challenging, and does not readily allow for detecting mixed-type infections
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