title: Sequence variation and phylogenetic analysis of the 5' terminus of hepatitis G virus.
abstract: We determined the nucleotide and deduced amino acid sequence of the 5' terminus of the hepatitis G virus (HGV) genome from isolates of varied geographical origins. Our analysis showed that the putative 5' non-coding region (NCR) contains several blocks of highly conserved sequences that may be useful for the development of a reverse transcriptase-polymerase chain reaction (RT-PCR) assay for detection of HGV RNA. Overall, the degree of conservation within the 669-nucleotide (nt) 5'terminal sequence was found to range from 99.5% to 86% sequence identity. We also showed that the HGV NCR from some isolates contained conserved insertions or deletions that altered the translational reading frames at the 5'-end of the genome, resulting in different sizes of predicted polyproteins encoded by genomes of individual isolates. Specifically, the insertions/deletions affected the size of the peptide preceding the putative first envelope (E1) protein. Phylogenetic analysis of the nucleotide sequences suggested that the isolates examined can be classified into distinct groups that may be useful for studying the molecular evolution of HGV and possible relationships between isolate sequence characteristics and infection patterns.
authors.affiliation: Genelabs Technologies, Inc., Redwood City, California, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Linnen
authors.forename: K
authors.initials: K
authors.lastname: Fung
authors.forename: K E
authors.initials: KE
authors.lastname: Fry
authors.forename: M
authors.initials: M
authors.lastname: Mizokami
authors.forename: K
authors.initials: K
authors.lastname: Ohba
authors.forename: J M
authors.initials: JM
authors.lastname: Wages
authors.forename: Z Y
authors.initials: ZY
authors.lastname: Zhang-Keck
authors.forename: K
authors.initials: K
authors.lastname: Song
authors.forename: J P
authors.initials: JP
authors.lastname: Kim
mesh_terms: D017498:Adenovirus E1 Proteins / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements; D004279:DNA, Viral / Q000032:analysis / Q000737:chemistry / Q000235:genetics*; D018067:Flaviviridae / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D017353:Gene Deletion; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017498:Adenovirus E1 Proteins; D004251:DNA Transposable Elements; D004279:DNA, Viral