Discrepancy between HCV structural and non structural genes in Georgian genotype two patients

Correct identification of hepatitis C genotypes is an important diagnostic tool, which guarantees further selection of adequate treatment regimen and correct duration. Ideal approach for accurate genotyping is amplification of both structural and non structural parts of HCV genome. As different methods, which use either one or another region for HCV genotyping sometimes lead to indeterminate genotype and subtype results. Therefore, it is of importance to compare HCV genotyping results based on two different genomic regions. As part of this study, remnant 108 specimens, with previous history of successful genotype identification by 5'UTR/core Versant HCV genotyping kit, were retrospectively analyzed. "In house" HCV real time PCR based method that amplifies parts of NS5B region was used for this purpose. Based on our data, genotyping calls were concordant between genotype one and genotype three specimens group in both regions. However, discrepancy was evident among genotype 2 group. Of 25 specimens originally typed as genotype 2 in structural region, only 7 was confirmed in non structural region, remaining 18 specimens were typed as 1b. Therefore, the discordance rate between structural and non structural regions for genotyping call among genotype two was 72%. Our data showed highly discordant structural and non structural genome for genotype two identification in our specimens. We propose that this phenomenon might be due to the recombination event between genotype two and genotype one. Possible circulation of this strain in Georgia stresses the need for detailed sequencing and phylogenetic analyses of these specimens in both structural and non structural parts of HCV genome.