ViralZone: a knowledge resource to understand virus diversity

Abstract

The molecular diversity of viruses complicates the interpretation of viral genomic and proteomic data. To make sense of viral gene functions, investigators must be familiar with the virus host range, replication cycle and virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge with genomic and proteomic sequences. ViralZone web resource (www.expasy.org/viralzone/) provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increase of virus sequences. Moreover ViralZone offers a complete set of detailed and accurate virion pictures.

Figure 1.

Diversity of viral replication: example of Ebolavirus versus Herpesvirus. (A) Ebolavirus is a negative single stranded RNA virus which replicates in the cytoplasm. It enters target cell by endocytosis, then penetrates into the cytoplasm by low pH fusion in the endosome. The viral RNA-dependent-RNA polymerase transcribes and replicates the viral genome in cell cytoplasm. Assembly and budding occur at the plasma membrane. (B) Herpes Simplex virus is a double stranded DNA virus which enters target cell by fusion at the plasma membrane, releasing the viral capsid in the cytoplasm. The capsid is transported to the nucleus where it injects the genomic DNA into the cell's nucleus. The viral genome circularises and conducts transcription and replication. New viral capsids are assembled in the nucleus, and bud into the endogenous reticulum (ER). These new virions fuse with ER membranes to release capsids into the cell cytoplasm. A second budding occurs at cell vesicle, and new virions are eventually released by exocytosis.

Figure 2.

(A) ViralZone Baltimore Index. (B) Taxonomic index for ssRNA(+) viruses, classified by order, family then genus. Colour spots indicate the host infected by each virus genera: pink for human and other vertebrates, purple for non-human vertebrates, green for plants, yellow for invertebrates, orange for eukaryotic microorganism, and blue for prokaryotes; (C) Genus fact sheet. (D) List of viruses referenced in UniProtKB/Swiss-Prot along with correspondent protein entries displayed by default under the fact sheet. (E) The list of entries sorted by protein names. (F) Alignment obtained after selection of protein entries in (E). (G) Each Swiss-Prot protein entry gives a direct link to UniProt web site to access to the full details of protein annotation.

Figure 3.

This page of ViralZone displays small virion picture for all dsDNA viruses (www.expasy.org/viralzone/all_by_species/748.html). Clicking on virus family or orphan genus name gives access to the virus description page, with full size picture of virion.