African origin of GB virus C determined by phylogenetic analysis of a complete genotype 5 genome from South Africa

• Published in: Journal of general virology Vol. 86; no. 6; pp. 1729 - 1735
• Main Authors: Muerhoff, A. Scott, Leary, Thomas P, Sathar, Mahomed A, Dawson, George J, Desai, Suresh M
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.06.2005; Society for General Microbiology
• Subjects: Biological and medical sciences; Flaviviridae Infections - virology; Fundamental and applied biological sciences. Psychology; GB virus; GB virus C - classification; GB virus C - genetics; Genome, Viral; Genotype; Hepatitis, Viral, Human - virology; Humans; Microbiology; Miscellaneous; Molecular Sequence Data; Phylogeny; South Africa; Viral Envelope Proteins - genetics; Virology; South Africa; Africa; Virus; Origin; Microbiology; Genotype; Phylogeny; Flaviviridae; Genome; Flavivirus; African; Virology; Hepatitis G virus
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/vir.0.80854-0

1 Infectious Diseases Research and Development, Abbott Diagnostics Division, Abbott Laboratories, Dept 9NB, Bldg AP20-4, 100 Abbott Park Road, Abbott Park, IL 60064-6015, USA 2 Infectious Disease Unit, Nelson R. Mandela School of Medicine, Doris Duke Research Institute, University of KwaZulu-Natal, South Africa Correspondence A. Scott Muerhoff scott.muerhoff{at}abbott.com GB virus C (GBV-C), a positive-strand RNA virus, currently infects approximately one-sixth of the world's population. This virus exists as a collection of genotypes whose global distribution correlates with geographical origin. Genotyping of GBV-C isolates by phylogenetic analysis has relied upon the use of 5'-untranslated region (5'-UTR) sequences, however, complete genome sequences are used to demonstrate definitively their existence and geographical correlation. Initial identification of the fifth genotype from South Africa was based upon phylogenetic analysis of the 5'-UTR. It was sought to confirm this classification by analysis of full-length E2 genes from South African isolates and by analysis of a complete genotype 5 genome. Analysis of full-length E2 genes from 28 GBV-C-infected South African individuals revealed the existence of a unique group of 18 isolates, distinct from the other four genotypes. Bootstrap analysis provided strong support (95 %) for this fifth group. The remaining isolates were either genotype 1 ( n =8) or 2 ( n =2). Analysis of human E2 gene sequences, with the E2 gene from the chimpanzee variant GBV-C tro included as the outgroup, produced a tree rooted on the genotype 1 branch. The complete genome nucleotide sequence of South African genotype 5 isolate D50 was determined. Phylogenetic analysis of the 5'-UTR and open reading frame produced congruent trees that grouped the sequences into five major genotypes. Inclusion of the corresponding region of the chimpanzee isolate GBV-C tro in the analysis produced trees rooted on the branch leading to the genotype 5 isolate D50, suggesting an ancient African origin of GBV-C. The GenBank/EMBL/DDBJ accession numbers of the sequences reported in this paper are AY951953–AY951980 and AY949771 . HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS INT J SYST EVOL MICROBIOL MICROBIOLOGY J GEN VIROL J MED MICROBIOL ALL SGM JOURNALS Copyright © 2005 by the Society for General Microbiology.