Fig. 3

Specific amplification with subtype-specific oligonucleotides in patient samples infected with HCV. Ten viral RNAs that correspond to subtypes 1a, 1b, 2a, 2b, 2c, 2j, 3a, 4a, 4d, 4f (left colum) isolated from HCV-infected patients were subtyped using next-generation sequencing [34], and used to amplify NS3-, NS5A-, and NS5B-coding regions with subtype-specific oligonucleotides. Viral RNA of each subtype was confronted with oligonucleotide pairs of the subtypes under study (listed at the top, below the genomic region). A total of 120 oligonucleotide primers out of 280 were tested. Amplifications correspond to RT-PCR 1 and PCR 1.2 in the NS3-coding region, RT-PCR 2 and PCR 2.2 in the NS5A-coding region, and RT-PCR 4 and PCR 4.1 in the NS5B-coding region, as depicted in Fig. 2. C-, negative control, amplification without RNA. Conditions of amplifications are detailed in Materials and Methods