Detection of hepatitis C virus natural recombinant RF1_2k/1b strain among intravenous drug users in Uzbekistan.
OBJECTIVE
A series of recent studies have indicated the presence of natural intergenotypic recombinant hepatitis C virus (HCV) strains in distinct parts of the world. The majority of the current genotyping methods are based on analysis of either 5'UTR, structural (Core/E1/E2) or non-structural (NS5B) genomic regions of the virus.


METHODS
In the present study, based on both structural and non-structural regions, we determined the genotype of 55 anti-HCV-positive intravenous drug users (IDUs) in Uzbekistan.


RESULTS
HCV-3a (67.3%) was the most prevalent genotype in this cohort, followed by HCV-1b (27.3%). A discrepancy in results was observed between structural and non-structural regions in one case (1.8%). Phylogenetically this strain was related to the previously reported RF1_2k/1b variant. Based on accumulated sequences, specific primers were designed for polymerase chain reaction (PCR) spanning the tentative intergenotypic crossover point of RF1_2k/1b. The sensitivity and specificity of the method were assessed using generated template clones of HCV-1b, 2a, 2 k and RF1_2k/1b. The method was applied to 55 cases in the present study and only one case showed a positive result, indicating that in these individuals, the variant is not present as a minor quasispecies clone.


CONCLUSIONS
In conclusion, the finding of RF1_2k/1b in Central Asia indicates that the variant has wide geographic distribution. The PCR-based screening method developed in this study should be useful in further epidemiological and clinical studies on the recombination phenomenon in HCV.
Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Nagoya, Japan, and National Reference Laboratory and Research Institute of Virology, Ministry of Public Health, Tashkent, Uzbekistan.
Fuat
F
Kurbanov
Yasuhito
Y
Tanaka
Dildora
D
Avazova
Anis
A
Khan
Fuminaka
F
Sugauchi
Nataliya
N
Kan
Dinara
D
Kurbanova-Khudayberganova
Aziza
A
Khikmatullaeva
Erkin
E
Musabaev
Masashi
M
Mizokami