Background: The first HCV recombinant form, RF2k/1b was initially described in Russia and has since been identified from patients in Ireland, France, Estonia, Uzbekistan and Cyprus. Many of these patients were originally from the country of Georgia. Full genome sequencing studies revealed that this form shares the structural part of the HCV genome from genotype 2 and the non-structural part from genotype 1. As the routine method for genotype identification in Georgia is by the Versant HCV Genotype v2 kit, which amplifies structural Core and 5’UTR regions, nucleotide sequences in non-structural regions will be missed.Therefore, we conducted a small study to compare two genomic regions of HCV for the purpose of HCV recombinant form identification.
Methods: We retrospectively sequenced HCV non-structural region 5B (NS5B) in remnant specimens collected from 72 HCV infected Georgian patients with genotypes previously determined with the Versant HCV Genotype v2 kit as: 32 (44.4%) genotype 1, 21 (29.1%) genotype 2 and 19 (26.3%) genotype 3. Of those patients thirty six patient had underwent PEG/RBN treatment.
Results: A portion of the NS5B region was sequenced among all 72 specimens, with concordant non-structural/structural results for most genotype 1 and all genotype 3 specimens. Of 21 genotype 2 specimens, 16 showed similarities to genotype 1b. A phylogenetic tree shows that 15 sequences of discordant sequences formed a clade with RF2k/1b reference sequences chosen from different countries. Remaining discordant sequence was found outside the RF2k/1b sub-branch and formed a cluster within genotype 1b. Our findings reveal that among Georgian patients with HCV genotype 2, 76.1% of viral sequences were similar to genotype1b and phylogenetically distinct from genotype 2.
Conclusions: Since 21 specimens were considered genotype 2 based on standard HCV genotyping methods; there is a need for genotyping in two genomic regions at least for genotype 2. The high prevalence of possible RF2k/1b in our small sample group stresses the need of further studies, as this form might circulate in Georgia widely and may alter treatment options and/or duration as it shares non-structural regions with genotype 1 and may be as difficult to treat as this genotype.
Figure 1. Phylogenetic Tree Constructed Based on the Partial Segment of the NS5B Region.
Reference recombinant strains RF 2k/1b in shown red diamond, genotype 1 in green, genotype 3 in purple and 2 in blue. Reference sequences are shown by their isolate name and country. Numbers at the nodes show the percentages of bootstrap values.