BACKGROUNDThe study aimed to investigate hepatitis C virus (HCV) specific markers in chronically infected children. The main objective was to explore the patterns of marker variability.METHODSHCV RNA, core antigen, anti-HCV IgM, and antibodies to individual viral proteins were detected using commercially available assays or experimental ELISA. RNA genotyping and recombination were performed by sequencing.RESULTSHCV RNA and core antigen were detected in serum samples of all children (N.=100). Anti-HCV IgM, anti-NS4AB IgG, and anti-NS5A IgG were revealed less often than antibodies to core and NS3 proteins. To elucidate the cause of this finding, all subjects were divided into 4 groups differing in hepatitis duration. It was anti-NS4AB only whose detection depended on the infection duration. A trend was established that the longer the hepatitis duration, the more frequently anti-HCV IgM was observed. No significant impact of HCV RNA load and NS4A/NS4B amino acid substitutions on anti-NS4AB IgG detection was found. The increase HCV genotype 3 was observed among children infected after 2000. The earliest case of infection caused by HCV intergenotype recombinant RF1_2k/1b was identified in a child vertically infected in 1997.CONCLUSIONSHCV genotypes and subtypes were found to be variable virus specific markers in children infected in 1997-2015. Over the period, there has been a trend to change the dominant HCV subtype and appearance of recombinant RF1_2k/1b in children. Among humoral markers, anti-NS4AB revealing is depended on chronic hepatitis C duration, while for anti-HCV IgM, only a trend was established. The detection of anti-NS4AB can be helpful in assessing the duration of chronic hepatitis C.