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Fig. 1 | BMC Infectious Diseases

Fig. 1

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

Fig. 1

Design of subtype-specific oligonucleotides. A total of 1,936,116 nucleotides at 1,638 positions along the HCV genome belonging to the ten HCV subtypes under study were analyzed. a Example of an intra-subtype comparison from position 3392 to position 3406 within the NS2-coding region (sequence in gray at the top) for HCV subtype 1b. The nucleotide numbering is based on the sequence of HCV strain H77 (GenBank accession AF009606). Numbers in boxes represent the number of sequences that for each position have the nucleotides written on the left grey column. Positions have been defined as conserved (in red) when they contain a single nucleotide type, partially conserved (in orange) when they contain at least two nucleotides (but only one of them with a frequency above 20% of the total number of sequences), and variable (in green) when two nucleotide types have a frequency above 20% of the total number of sequences. Only in variable positions a mixture of two nucleotides is considered to define the column (see the bottom raw termed “Final sequence”). b Example of an inter-subtype comparison from position 3392 to position 3406 within the NS2-coding region (sequence in gray at the top). Final sequences —defined as described in (A) for the HCV subtypes 1a, 1b, 2a, 2b, 2c, 2j, 3a, 4a, 4d, and 4f— were compared to define positions that are discriminatory for a specific subtype and/or genotype (color codes given in the bottom box). Red circles highlight the nucleotides specific for a defined subtype and/or genotype. Excel file including all comparisons will be made available upon request

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