Genotyping Hepatitis B virus from whole- and sub-genomic fragments using position-specific scoring matrices in HBV STAR.

Hepatitis B virus (HBV) genomes have been classified into eight genotypes based on phylogenetic analysis of sequence variation. Identifying and tracking the movement of HBV genotypes is important in terms of both monitoring infection rates and predicting disease and treatment. An HBV genotyping tool has been developed that compares query sequences with position-specific scoring matrices representing the eight HBV genotypes. This tool (hbv star) is rapid, robust and accurate and assigns genotype based on a statistically defined scoring model. hbv star confidently assigned 90% of 590 full-length HBV genomes to an HBV genotype (Z score >2.0). Thirty-two of the residual 48 sequences were identified as non-human primate viruses and 16 sequences were identified as recombinant or putative recombinants. Receiver-Operated Characteristic (ROC) analysis was used to compare the accuracy of genotype prediction using basal core promoter sequences and surface and core genes with the accuracy achieved by using full-length sequences. A web interface to hbv star is available at http://www.vgb.ucl.ac.uk/starn.shtml.

[1]  A. Harrison,et al.  A statistical model for HIV-1 sequence classification using the subtype analyser (STAR) , 2005, Bioinform..

[2]  P. Coursaget,et al.  Genetic Diversity of Hepatitis B Virus Strains Derived Worldwide: Genotypes, Subgenotypes, and HBsAg Subtypes , 2004, Intervirology.

[3]  P. Angus,et al.  Clinical Emergence of Entecavir-Resistant Hepatitis B Virus Requires Additional Substitutions in Virus Already Resistant to Lamivudine , 2004, Antimicrobial Agents and Chemotherapy.

[4]  I. Williams,et al.  Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London. , 2004, AIDS research and human retroviruses.

[5]  M. Mizokami,et al.  Hepatitis B Virus Genotypes and Hepatocellular Carcinoma in Japan , 2003, Intervirology.

[6]  Ching-Lung Lai,et al.  Prevalence and clinical correlates of YMDD variants during lamivudine therapy for patients with chronic hepatitis B. , 2003, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[7]  K. Koike,et al.  Hepatitis B virus genotypes and hepatocellular carcinoma in Japan. , 2001, Gastroenterology.

[8]  Makoto Nakanishi,et al.  Hepatitis B Virus Genotype Distribution among Chronic Hepatitis B Virus Carriers in Shanghai, China , 2001, Intervirology.

[9]  W. Delaney,et al.  Resistance of Hepatitis B Virus to Antiviral Drugs: Current Aspects and Directions for Future Investigation , 2001, Antiviral chemistry & chemotherapy.

[10]  Ding‐Shinn Chen,et al.  Hepatitis B genotypes correlate with clinical outcomes in patients with chronic hepatitis B. , 2000, Gastroenterology.

[11]  K. Lole,et al.  Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination , 1999, Journal of Virology.

[12]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[13]  J. Felsenstein.  Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. , 1996, Methods in enzymology.

[14]  U. Akarca,et al.  Mutations in the pre-core region of hepatitis B virus serve to enhance the stability of the secondary structure of the pre-genome encapsidation signal. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Soulier,et al.  Monoclonal antibodies to HBsAg: a study of their specificities for eight different HBsAg subtypes. , 1983, Developments in biological standardization.