Molecular characterization of the 5? non-coding region of South African GBV-C/HGV isolates: Major deletion and evidence for a fourth genotype
✍ Scribed by Tucker, Timothy J.; Smuts, Heidi; Eickhaus, Peter; Robson, Simon C.; Kirsch, Ralph E.
- Publisher
- John Wiley and Sons
- Year
- 1999
- Tongue
- English
- Weight
- 226 KB
- Volume
- 59
- Category
- Article
- ISSN
- 0146-6615
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✦ Synopsis
GB virus C/hepatitis G virus (GBV-C/HGV) has been characterised as a novel flavivirus, and to date three known genotypes have been cloned. Greater genetic variation of GBV-C/HGV has been demonstrated in West African isolates, but no major deletions have been shown in the 5Ј non-coding region (NCR). The 5ЈNCR regulates protein translation via an internal ribosomal entry site (IRES). We cloned, sequenced, and analysed a 344-bp polymerase chain reaction (PCR) product, representing >60% of the 5ЈNCR, from 32 GBV-C/HGV PCR-positive volunteers. Wildtype virus amplicons were detected in all samples. However, 5/32 (15.6%) also amplified another fragment of between 205 and 231 bp. Sequence analysis showed all cloned PCR fragments to be GBV-C/HGV-specific. A typical deletion of 113-131 bp with minor variation was detected in isolates generating the smaller bands. RNA secondary structure analysis showed the deletions to be over domains II and III. This finding suggests that nucleotides 303-444 may be non-essential for 5ЈNCR functioning. Phylogenetic analysis demonstrated a novel fourth South African genotype, distinct from genotypes 1-3 with DNA distances of >0.1000. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) values for the wild-type and mutant samples were normal. This study documents the first major deletion in the 5ЈNCR of GBV-C/HGV, and suggests that bases 303-444 may not be essential for viral replication and ribosomal entry.