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The prevalence study and the characterization of hepatitis C virus (HCV) have been carried out in the Philippines and the sequence determination of 5'-untranslated region (5'-UTR)-Core and NS5B regions of HCV was performed in this study. An HCV strain (SE-03-07-1689) collected in Metro Manila, Philippines, belonged to discordant subtypes, 2b and 1b in 5'-UTR-Core and NS5B regions, respectively. The 9.3kb-sequence of this strain including the entire open reading frame were compared with those of the reference strains retrieved from the HCV sequences database (GenBank/EMBL/DDBJ) and indicated a recombination event.The computation of the sequence similarity mapped a crossover point within NS3region. This is the second report on the inter-genotype recombinant of HCV and the third one when an intra-genotype recombinant is included. This recombinant strain, SE-03-07-1689, is tentatively designated as RF3_2b/1b according to the suggestions used for other two HCV recombinants.

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