Discrimination of hepatitis G virus/GBV-C geographical variants by analysis of the 5' non-coding region

DB Smith, N Cuceanu, F Davidson, LM Jarvis, JL Mokili, S Hamid, CA Ludlam and P Simmonds Department of Medical Microbiology, University of Edinburgh, Medical School, UK. Donald.B.Smith@ed.ac.uk We have investigated the ability of different subgenomic fragments to reproduce the phylogenetic relations...

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Bibliographic Details
Published in:Journal of general virology 1997-07, Vol.78 (7), p.1533-1542
Main Authors: Smith, DB, Cuceanu, N, Davidson, F, Jarvis, LM, Mokili, JL, Hamid, S, Ludlam, CA, Simmonds, P
Format: Article
Language:English
Subjects:
Base Sequence
DNA, Viral - chemistry
DNA, Viral - genetics
Female
Flaviviridae - classification
Flaviviridae - genetics
Genetic Variation
Genome, Viral
hepatitis G virus
Hepatitis, Viral, Human - virology
Humans
Introns
Male
Molecular Sequence Data
Nucleic Acid Conformation
Phylogeny
RNA, Viral
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Summary:DB Smith, N Cuceanu, F Davidson, LM Jarvis, JL Mokili, S Hamid, CA Ludlam and P Simmonds Department of Medical Microbiology, University of Edinburgh, Medical School, UK. Donald.B.Smith@ed.ac.uk We have investigated the ability of different subgenomic fragments to reproduce the phylogenetic relationships observed between six complete genome sequences of GBV-C/hepatitis G virus (HGV). While similar relationships were observed following analysis of part of the 5' non- coding region (5'NCR), for the coding region they were not accurately reproduced for some large fragments or for the majority of fragments of 300 or 600 nucleotides. Analysis of 5'NCR sequences from a large number of isolates, including newly obtained sequences from Pakistan, Zaire and Scotland, produced separate groupings of Asian, African and European/North American variants. These groupings are associated with specific polymorphisms in the 5'NCR, many of which were covariant and consistent with a proposed secondary structure for this region. The relatively low level of amino acid sequence variation observed between these geographically and phylogenetically defined groups of variants suggests that they are unlikely to display significant biological differences.
ISSN:0022-1317
1465-2099
DOI:10.1099/0022-1317-78-7-1533