Discrepancy of hepatitis C virus genotypes as determined by phylogenetic analysis of partial NS5 and core sequences

✍ Scribed by Yun, Zhibing; Lara, Claudia; Johansson, Bo; Lorenzana de Rivera, Ivette; Sönnerborg, Anders

• Publisher: John Wiley and Sons
• Year: 1996
• Tongue: English
• Weight: 475 KB
• Volume: 49
• Category: Article
• ISSN: 0146-6615
• DOI: 10.1002/(sici)1096-9071(199607)49:3<155::aid-jmv1>3.0.co;2-3

✦ Synopsis

The use of phylogenetic analyses of partial NS5 and core regions for hepatitis Cvirus (HCV) genotyping was evaluated by analysing seven Honduran and 24 European HCV strains. Core primers were designed with which HCV genotypes 1, 2, and 3 were readily amplified. The reliability of phylogenetic analysis of a 11 I-bp core sequence was verified by comparing the typing results with those obtained using the whole core gene of 52 reference strains. Accordant genotypes ( l a , 1 b, 2b. and 3a) were obtained when phylogenetic analyses were undertaken on both the partial core and a 222-bp NS5 sequence in all of the European HCV strains. Genotypes l a , Ib, and 3a were identified among the Honduran strains by phylogenetic analysis of the partial NS5 sequence. Interestingly, two of three Honduran type 3a strains, as determined by the NS5 sequence analysis, turned out to be type l a by core sequence analysis. These two strains were also classified as type l a , but not 3a, by a core typespecific PCR. Furthermore, the E2/NS1 regions were similar to HCV-PT, a representative strain of genotype l a . The results indicate that chimera1 HCV strains exist, although in most cases a good concordance is found when phylogenetic analysis of partial core and NS5 sequences are used

Methods

Patients Sera were obtained from eight anti-HCV positive patients in Honduras. Three patients were polytransfused (HO 2, HO 3, HO 4), two patients were detected in connection with blood donation (HO 1, HO 7), and three were prison inmates (HO 5, HO 6, HO 8). Twenty-four HCV strains from Sweden and Norway were also analysed together with the Honduran strains.

Reverse Transcription and PCR

HCV RNA was extracted from 100 p1 serum B u n et al., 19931 and subjected to a combined RT-PCR, using