[Study of the 3'noncoding region of Chinese hepatitis C virus genome].
OBJECTIVE
To analyze the 3' noncoding region (3' NCR) of HCV genome from Chinese hepatitis C patients so as to facilitate further study of mechanism of HCV gene replication.


METHODS
Two different strategies were employed to amplify the full-length of the 3' noncoding region of HCV genome from sera of HCV infected patients in Shanghai area: one was to amplify the full-length fragment directly by nested PCR and the other amplify two overlapping fragments. The PCR products were further analyzed by sequencing and nucleotide alignments. A HCV genome 3'NCR based RT-PCR was developed and its specificity and sensitivity for HCV RNA detection in sera was compared with the established 5'NCR based RT-PCR.


RESULTS
Sequence analysis showed that Chinese HCV genomic 3' NCR consists of three parts: the 5' region, poly (U-UC) tract and the 98-base region. Sequence alignments revealed that, while the 98-base regions were completely conserved in different isolates and were identical to the reported sequences, the poly (U-UC) region shared highly diversities. A high degree of concordance(95%) between the 3'NCR and 5'NCR RT-PCR for detection of HCV RNA in sera was found.


CONCLUSIONS
The high conservation at the 3' NCR(98 bases) of HCV genome among different isolates indicated that this region may be critical for HCV gene replication The 3'NCR based RT-PCR may be a useful addition to available systems to diagnosis HCV infection.
Lan
S
S
Department of Molecular Virology, Shanghai Medical University, Shanghai 200032.
Yuan
Z
Z
Hu
Y
Y
D020413:3' Untranslated Regions / Q000235:genetics*; D020121:5' Untranslated Regions / Q000235:genetics; D001483:Base Sequence; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000097:blood; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014779:Virus Replication
D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D012367:RNA, Viral