The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a given host. A database allowing researchers to investigate the genetic and structural variability of all available HCV sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development. We describe here the European Hepatitis C Virus Database (euHCVdb, ), a collection of computer-annotated sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as well as three-dimensional (3D) molecular models of proteins. A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses. As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses.

Toxoplasma gondii is an obligate intracellular parasite that contains a relic plastid, called the apicoplast, deriving from a secondary endosymbiosis with an ancestral alga. Metabolic labelling experiments using [14C]acetate led to a substantial production of numerous glycero- and sphingo-lipid classes in extracellular tachyzoites. Syntheses of all these lipids were affected by the herbicide haloxyfop, demonstrating that their de novo syntheses necessarily required a functional apicoplast fatty acid synthase II. The complex metabolic profiles obtained and a census of glycerolipid metabolism gene candidates indicate that synthesis is probably scattered in the apicoplast membranes [possibly for PA (phosphatidic acid), DGDG (digalactosyldiacylglycerol) and PG (phosphatidylglycerol)], the endoplasmic reticulum (for major phospholipid classes and ceramides) and mitochondria (for PA, PG and cardiolipid). Based on a bioinformatic analysis, it is proposed that apicoplast produced acyl-ACP (where ACP is acyl-carrier protein) is transferred to glycerol-3-phosphate for apicoplast glycerolipid synthesis. Acyl-ACP is also probably transported outside the apicoplast stroma and irreversibly converted into acyl-CoA. In the endoplasmic reticulum, acyl-CoA may not be transferred to a three-carbon backbone by an enzyme similar to the cytosolic plant glycerol-3-phosphate acyltransferase, but rather by a dual glycerol-3-phosphate/dihydroxyacetone-3-phosphate acyltransferase like in animal and yeast cells. We further showed that intracellular parasites could also synthesize most of their lipids from scavenged host cell precursors. The observed appearance of glycerolipids specific to either the de novo pathway in extracellular parasites (unknown glycerolipid 1 and the plant like DGDG), or the intracellular stages (unknown glycerolipid 8), may explain the necessary coexistence of both de novo parasitic acyl-lipid synthesis and recycling of host cell compounds.

Part of the effort to develop hepatitis C-specific drugs and vaccines is the study of genetic variability of all publicly available HCV sequences. Three HCV databases are currently available to aid this effort and to provide additional insight into the basic biology, immunology, and evolution of the virus. The Japanese HCV database (http:// s2as02.genes.nig.ac.jp) gives access to a genomic mapping of sequences as well as their phylogenetic relationships. The European HCV database (http://euhcvdb.ibcp.fr) offers access to a computer-annotated set of sequences and molecular models of HCV proteins and focuses on protein sequence, structure and function analysis. T he hepatitis C virus (HCV) has infected approximately 170 million people worldwide. HCV infection is cleared in about 25% of cases, 1,2 and in the rest results in chronic infection. Chronic HCV infection can lead to cirrhosis and liver cancer, and is the leading cause of liver transplantation in the United States. A recent Canadian study 3 estimated that lifetime HCV-associated mortality is around 1 in 8; a much larger number (an estimated 1 in 4) will develop cirrhosis of the liver. Most likely this number will be higher in less developed countries. With 170 million people infected worldwide, this means 20 million HCVrelated deaths in the next few decades.HCV is a positive-sense RNA virus with a genome of Ϸ10 kb, which encodes a single polyprotein of Ϸ3000 amino acids (aa) that is cleaved into three structural proteins (core, Envelope E1 and E2), the p7 protein whose function has not been determined, and six non-structural proteins (NS2, NS3, NS4A, NS4B, NS5A and NS5B). It has been classified as a hepacivirus, in of the Flaviviridae family, which also includes flaviviruses (West Nile, Japanese encephalitis and yellow fever viruses) and pestiviruses (bovin viral diarrhea and hog cholera virus). HCV shares some structural features with these viruses. However, the genetic distance between HCV and other flaviviruses is large enough that HCV cannot be meaningfully aligned to its flavivirus "relatives" over its entire genome 4 (also see http://hcv.lanl.gov/content/hcv-db/GET_ALIGNMENTS/ flavi-align.html), and it also shares structural features with the pestivirus family.HCV is subdivided into six genotypes and about 80 subtypes on the basis of nucleotide sequence identity. 5 In addition to genotypes, HCV exists within its hosts as a pool of genetically distinct but closely related variants referred to as quasispecies. 6 While there is limited knowledge about the immunogenicity of HCV, it is widely expected that both the generation of escape and resistance mutations and the high variability itself will create formidable problems for drug and vaccine design. 7 This paper discusses three HCV databases available worldwide, in order of seniority: the Japanese HCV map and phylogeny database, the European HCV sequence and molecular models database and the Los Alamos HCV sequence and immunology databases. We will first describe the three databases, highlighting comm...

No abstract