Database Commons

a catalog of worldwide biological databases

AIM: Currently, approximately 44 000 hepatitis C virus (HCV), 11 000 hepatitis B virus (HBV), and 1600 hepatitis E virus (HEV) sequences are available at the International Nucleotide Sequence Database Collaboration (INSDC, previously known as DDBJ/EMBL/GenBank), and the number of these virus sequences is growing rapidly. However, since INDSC is not specialized to hepatitis viruses, it is difficult to retrieve information of virological or clinical interests from it. Thus, it is quite worthwhile to construct a specialized database for the hepatitis virus sequences and to make it accessible to researchers worldwide.
METHODS: We developed a WWW-based database hepatitis virus database (HVDB), which contains all the HCV, HBV, and HEV sequences available at INSDC. In the HVDB, all piece sequences obtained from INSDC are arranged to the genomesequence of each virus. Also given in the database are the phylogenetic relationships of each locus on the genome among variants for each virus.
RESULTS: Users of the database can easily retrieve entries (sequences with annotations) of the specific genotype by referring to the phylogenetic relationships or those of specific loci by referring to the genome map information. HVDB provides users with a tool for phylogenetic analysis that can be used in combination with the data retrieval tools.
CONCLUSION: The latest release is publicly accessible at the HVDB website: http://s2as02.genes.nig.ac.jp.

Hepatitis C virus (HCV) is a member of the virus family Flaviviridae. At present HCV is classified into a discrete hepacivirus genus and is represented by six clades according to genome sequencing. Each clade is further divisible into subtypes, which may prove important for the study of clinical differences and epidemiological studies. Limited homology also exists with hepatitis G/GB viruses, despite the fact that the hepatotropic nature of the latter agents remains contentious. The variability amongst the six HCV clades is less than that observed between the four serotypes of dengue, suggesting that each clade may represent a distinct virus were tests such as plaque neutralization to become available for delineating HCV isolates. The distribution worldwide varies, with Clades 1 and 2 predominating in most regions-an important consideration for the development of any vaccine. In addition, the clade distribution among cohorts may vary according to age. Point source outbreaks of HCV, for example in large numbers of women inadvertently infected with HCV-contaminated anti-D globulin, offers an opportunity to study the evolution of HCV genotypes over several decades. Parallel studies in chimpanzees have shown that the hypervariable region of E2 may play a role in HCV immunity, with quasispecies rapidly replacing the predominant subtype as immunity develops to the initiating virus strain. There is some evidence that an IFN-sensitive motif exists in the NS5 gene which may have some predictive value in determining the likely outcome of IFN treatment. A database is available for all HCV sequences, together with information about their properties and guidance for the evaluation of new isolates (http://s2as02.genes.nig.ac.jp).