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Fig. 2 | BMC Infectious Diseases

Fig. 2

From: Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus

Fig. 2

Scheme of the RT-PCRs and PCRs designed to amplify HCV NS3-, NS5A, and NS5B-coding regions. Top: Scheme of the HCV genome with indication of nucleotide numbering (above the genome), and amino acid numbering for individual proteins (below the genome); numbering is defined according to [49]. Regions chosen to design the oligonucleotides described in the present study were those that include several subtype-specific positions, and that amplify regions that have been associated with DAA resistance. RT-PCRs labeled 1, 2 correspond to NS3-, NS5A- coding region, respectively, and 3, 4 and 5 to NS5B-coding region (numbers in black rectangles above the identified RT-PCR). Internal PCRs with different sizes can interrogate different positions in the HCV genome, and can be chosen according to the amplicon size restrictions imposed by the sequencing platform (several possibilities are depicted with identification numbers in white rectangles). Numbering at the beginning and at the end of each PCR (columns with colored numbers; color codes in the bottom box) correspond to the first and last amino acid of the amplicon, excluding oligonucleotides. When the number of the first amino acid is higher than the number corresponding to the reverse oligonucleotide means that the forward oligonucleotide is located in the gene upstream from the region to be amplified. Relative sizes of standard and internal PCRs for NS3, NS5A and NS5B are depicted comparatively in the white large boxes

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