Article Figures & Data
Figures
- FIG 1
Percentage of chimeras identified by the hybridization-based assay Versant HCV Genotype 2.0 and the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II.
- FIG 2
(a) Overview of genotype and subtype determination by the hybridization-based assay Versant HCV Genotype 2.0 and the real-time PCR-based assay cobas HCV GT in comparison to that by population-based sequencing. If genotype or subtype were consistent with sequencing results, calls were termed consistent; otherwise, the subtype was refined by the sequencing analysis. (b and c) Detailed subtype determination by the hybridization-based assay Versant HCV Genotype 2.0 (b) and by the real-time PCR-based-assay cobas HCV GT (c) in comparison to that by population-based sequencing. If subtype was consistent with sequencing results, calls were termed consistent; otherwise, the subtype was refined by the sequencing analysis.
- FIG 3
Schematic representation of viral recombination in HCV 2k/1b and targets for genotype typing/subtyping by the assays Versant HCV Genotype 2.0 (LiPA 2.0), cobas HCV GT, and Abbott RealTime HCV Genotype II. UTR, untranslated region; E, envelope protein; NS, nonstructural protein; gt, genotype.
Tables
- TABLE 1
Characteristics of different genotyping assays
Characteristic Genotyping assay Versant HCV Genotype 2.0 (LiPA 2.0) cobas HCV GT Abbott RealTime HCV Genotype II No. of detectable genotypes 1–6 1–6 1–6 Detectable subtypes 1a, 1b, 2b, 3a, 4b, 6a, 6 (c-l) 1a, 1b 1a, 1b Principle of the assay Reverse hybridization technology based on sequences from 5′-UTR for genotypes 1 to 6 and core region for genotype 1a, 1b, and 6c-l Real-time PCR targeting 5′-UTR, core and NS5B Real-time PCR targeting 5′-UTR for GT 1–6 identification and NS5B for GT1a and GT1b subtyping Chimera classification By different genotype detection in 5′-UTR compared to core By different genotype detection in 5′-UTR compared to core and to NS5B By different genotype detection in 5′-UTR compared to NS5B - TABLE 2
Genotype determination by different assays in comparison to population-based sequencingc
Genotype Population based sequencing Assay Versant HCV genotype 2.0 (LiPA 2.0) cobas HCV GT Abbott realtime HCV Genotype II All samples (n) 278 278 275a 48b 1 (n) 53 53 53 1a 0 0 0 1b 53 53 51 11 2 (n) 177 225 179 4 2a 49 2b 75 73 2c 38 2d 1 2f 3 2i 4 2k 6 2m 1 HCV indeterminate (n) 2 2/1 chimera (n) 48 0 43 31 2/1a 1 0 1 0 2b/1a 1 2/1b 47 0 42 29 2a/1b 1 2k/1b 46 Other 0 2 Identification of chimeras (total) (n [%]) 0 (0) 43 (90) 31 (65) ↵a Three measurements were invalid.
↵b Only assay results for chimeras detected by population-based sequencing were compared to results from population-based sequencing.
↵c Genotypes or subtypes detected by the different assays in Table 2 do not necessarily reveal that the variant was determined in accordance with sequence calling (except for the chimeras). These data are shown in Fig. 2.
