CHARACTERIZATION OF THE GENOMIC SEQUENCE OF TYPE-V (OR 3A) HEPATITIS-C VIRUS ISOLATES AND PCR PRIMERS FOR SPECIFIC DETECTION

We have identified four new hepatitis C virus (HCV) isolates whose gen omic RNA could be amplified by PCR using primers from the 5' untransla ted region (UTR), but the RNA could not be detected with genotype I to IV (or types 1 a, lb, 2a and 2b respectively)-specific core region-de rived primers. We compared the nucleotide sequences of the new isolate s from positions 65 to 1850 (3' end of 5' UTR, C, El and 5' end of E2/ NS1) and 8276 to 9394 (3' end of NS5 and 3' UTR) with those for genoty pes I to IV. The four isolates had the following characteristics: (i) the overall nucleotide sequence similarity between the four isolates w as 95 to 96 %, compared to 73 to 74 %, 73 %, 70 % or 69 to 70 % agains t genotypes I, II, III or IV, respectively; (ii) the sequence similari ty to other reported 'type V (3a)' isolates was 88 to 100 % ; (iii) th e hypervariable region 1 [(HVR)-1] was present but HVR-2 was absent wi thin the E2/NS1 region; (iv) only one in-frame termination codon was p resent for the presumed polyprotein; (v) the 3' UTR preceding a termin al poly(U) stretch was significantly shorter than in genotype I to IV isolates. We classified the four isolates as genotype V (3a), and sear ched for uniquely conserved nucleotide sequences that could be used fo r type-specific PCR. A core region-derived primer pair (no. 104V: 5'CG TAAAACTTCT GAACGGTC, sense and no. 339: 5'GCTGAGCCCA GGACCGGTCT, antis ense) was identified and successfully used to diagnose genotype V (3a) HCV infection.