Full-length GBV-C/HGV genomes from nine Japanese isolates: characterization by comparative analyses.
The genomes of nine GBV-C/HGV isolates from Japanese chronic hepatitis patients were fully sequenced and characterized. They shared 85% nucleotide sequence homology with previously characterized isolates from the US and West Africa. Homology studies and phylogenetic analyses showed that the Japanese isolates formed a third group distinct from the established groups 1 and 2. The genetic distances between the three groups of GBV-C/HGV were very similar to the distances between the two classical swine fever virus (CSFV) serotypes, which suggested that they might belong to a separate GBV-C/HGV serotype. Plot similarity analysis comparing the three groups exposed relatively conserved terminal non-coding regions. Hairpin structures predicted in the Japanese isolates are probably involved in viral replication. The region coding E1-E2-NS-2 showed the least similarity (80%); in HCV the similarity here is only 50% due to its hypervariability. NS-3 and NS-5b that respectively encode the helicase/protease and RNA-dependent RNA polymerase, had a high degree of amino acid homology, suggesting a high degree of functional constraint in this region. The NS-5b nucleotide sequence was highly conserved perhaps because of constraints from RNA secondary structure and/or an open reading frame in the negative strand.
Katayama
K
K
Basic Research Division, BioMedical Laboratories, Inc., Saitama, Japan.
Kageyama
T
T
Fukushi
S
S
Hoshino
F B
FB
Kurihara
C
C
Ishiyama
N
N
Okamura
H
H
Oya
A
A
D001483:Base Sequence; D018067:Flaviviridae / Q000235:genetics*; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012367:RNA, Viral / Q000737:chemistry
D012367:RNA, Viral