Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central America

• Published in: Journal of general virology 2002-08, Vol.83 (8), p.2059-2073
• Main Authors: Arauz-Ruiz, Patricia, Norder, Helene, Robertson, Betty H, Magnius, Lars O
• Format: Article
• Language: English
• Subjects: Asian Continental Ancestry Group; Central America - epidemiology; Genetic Variation; Genome, Viral; Genotype; Hepatitis B - epidemiology; Hepatitis B - ethnology; Hepatitis B - virology; Hepatitis B Surface Antigens - genetics; Hepatitis B virus - classification; Hepatitis B virus - genetics; Humans; Indians, North American; Molecular Sequence Data; Nicaragua - epidemiology; Phylogeny; Protein Precursors - genetics; Sequence Analysis, DNA
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/0022-1317-83-8-2059

Department of Virology, Swedish Institute for Infectious Disease Control, SE-171 82 Stockholm, Sweden 1 Louisiana State University-International Centre for Medical Research and Training, San José, Costa Rica 2 Laboratory Branch, Division of Viral Hepatitis, National Center for Infectious Diseases, Center for Disease Control and Prevention, Atlanta, GA 30333, USA 3 Author for correspondence: Lars Magnius. Fax [phone]. e-mail lars.magnius{at}smi.ki.se The complete genomes were sequenced for ten hepatitis B virus (HBV) strains. Two of them, from Spain and Sweden, were most similar to genotype D, although encoding d specificity. Five of them were from Central America and belonged to genotype F. Two strains from Nicaragua and one from Los Angeles, USA, showed divergences of 3·1–4·1% within the small S gene from genotype F strains and were recognized previously as a divergent clade within genotype F. The complete genomes of the two genotype D strains were found to differ from published genotype D strains by 2·8–4·6%. Their S genes encoded Lys 122 , Thr 127 and Lys 160 , corresponding to the putative new subtype adw3 within this genotype, previously known to specify ayw2 , ayw3 or, rarely, ayw4 . The complete genomes of the three divergent strains diverged by 0·8–2·5% from each other, 7·2–10·2% from genotype F strains and 13·2–15·7% from other HBV strains. Since pairwise comparisons of 82 complete HBV genomes of intratypic and intertypic divergences ranged from 0·1 to 7·4% and 6·8 to 17·1%, respectively, the three sequenced strains should represent a new HBV genotype, for which the designation H is proposed. In the polymerase region, the three strains had 16 unique conserved amino acid residues not present in genotype F strains. So far, genotype H has been encountered in Nicaragua, Mexico and California. Phylogenetic analysis of the complete genomes and subgenomes of the three strains showed them clustering with genotype F but forming a separate branch supported by 100% bootstrap. Being most similar to genotype F, known to be an Amerindian genotype, genotype H has most likely split off from genotype F within the New World.