@article{mbs:/content/journal/jgv/10.1099/0022-1317-74-11-2385, author = "Okamoto, Hiroaki and Tokita, Hajime and Sakamoto, Minoru and Horikita, Minoru and Kojima, Maki and Iizuka, Hisao and Mishiro, Shunji", title = "Characterization of the genomic sequence of type V (or 3a) hepatitis C virus isolates and PCR primers for specific detection", journal= "Journal of General Virology", year = "1993", volume = "74", number = "11", pages = "2385-2390", doi = "https://doi.org/10.1099/0022-1317-74-11-2385", url = "https://www.microbiologyresearch.org/content/journal/jgv/10.1099/0022-1317-74-11-2385", publisher = "Microbiology Society", issn = "1465-2099", type = "Journal Article", abstract = "We have identified four new hepatitis C virus (HCV) isolates whose genomic RNA could be amplified by PCR using primers from the 5′ untranslated region (UTR), but the RNA could not be detected with genotype I to IV (or types 1a, 1b, 2a and 2b respectively)-specific core region-derived primers. We compared the nucleotide sequences of the new isolates from positions 65 to 1850 (3′ end of 5′ UTR, C, E1 and 5′ end of E2/NS1) and 8276 to 9394 (3′ end of NS5 and 3′ UTR) with those for genotypes I to IV. The four isolates had the following characteristics: (i) the overall nucleotide sequence similarity between the four isolates was 95 to 96%, compared to 73 to 74%, 73%, 70% or 69 to 70% against genotypes I, II, III or IV, respectively; (ii) the sequence similarity to other reported ‘type V (3a)’ isolates was 88 to 100%; (iii) the hypervariable region 1 [(HVR)-1] was present but HVR-2 was absent within the E2/NS1 region; (iv) only one in-frame termination codon was present for the presumed polyprotein; (v) the 3′ UTR preceding a terminal poly(U) stretch was significantly shorter than in genotype I to IV isolates. We classified the four isolates as genotype V (3a), and searched for uniquely conserved nucleotide sequences that could be used for type-specific PCR. A core region-derived primer pair (no. 104V: 5′ CGTAAAACTTCT GAACGGTC, sense and no. 339: 5′ GCTGAGCCCA GGACCGGTCT, antisense) was identified and successfully used to diagnose genotype V (3a) HCV infection.", }