KEGG Virus Resource
KEGG Virus is a resource for integrating viruses and cellular organisms from an evolutionary perspective. Virus data are part of the PATHWAY, BRITE, KO, GENES, GENOME, NETWORK, DISEASE and DRUG databases as summarized below.
| Database | Virus data | Remark |
| PATHWAY | Disease pathway maps for viral infections Genetic information processing in viruses |
Manually created KEGG pathway maps |
| BRITE | Viral protein classifications | Manually created hierarchical classifications |
| KO | Viral proteins | Manually defined KOs (K number entries) for viral proteins |
| GENES | KEGG viruses in the NCBI taxonomy | Linked to virus gene (vg) entries created from NCBI RefSeq |
| GENOME | KEGG selected viruses | Completely sequenced viral genomes for human pathogens |
| NETWORK | Network variation maps for viral infections | Viruses viewed as perturbants to human signaling networks |
| DISEASE | Viral infectious diseases and genomes | KEGG DIESEASE (H number) entries |
| DRUG | Antivirals and targets | KEGG DRUG (D number) entries |
Pathway maps for viruses
The pathway maps for viral infections are interaction networks of both human proteins (colered in green and linked to human gene entries) and viral proteins (colored in blue and linked to virus KOs). The new category of genetic information processing in viruses will contain virus-specific genes and proteins.
| Category | Pathway map | Virus |
| Viral infections | 05166 Human T-cell leukemia virus 1 infection | HTLV-1 |
| 05170 Human immunodeficiency virus 1 infection | HIV-1 | |
| 05161 Hepatitis B | HBV | |
| 05160 Hepatitis C | HCV | |
| 05171 Coronavirus disease - COVID-19 | SARS-CoV-2 | |
| 05164 Influenza A | IAV | |
| 05162 Measles | MV | |
| 05168 Herpes simplex virus 1 infection | HSV-1 | |
| 05163 Human cytomegalovirus infection | HCMV | |
| 05167 Kaposi sarcoma-associated herpesvirus infection | KSHV | |
| 05169 Epstein-Barr virus infection | EBV | |
| 05165 Human papillomavirus infection | HPV | |
| 05203 Viral carcinogenesis | HBV, HCV, HPV, HTLV-1, KSHV | |
| Genetic information processing in viruses |
03230 Viral genome structure | HIV-1, HTLV-1, HBV, HCV, SARS-CoV-2 SARS-CoV, MERS-CoV, EBOV, MV |
Brite hierarchies and tables for viruses
Virus specific Brite hierarchy files and Brite table files are being developed.
| Category | Brite file |
| Functional classification | 03200 Viral proteins (all viral KOs) |
| 03210 Viral fusion proteins | |
| Taxonomy | 08620 KEGG viruses in the NCBI taxonomy (ICTV and Baltimore classifications) |
| 08621 KEGG viruses (simplified version with family, genus and species only) |
Virus genes and proteins
The virus category of the GENES database is generated from the RefSeq database and given KO annotation. RefSeq GeneID's are used as gene identifiers and the organism code "vg" (and T40000 identifier) is used for the entire set of viral genes. Each virus may be distinguished by the NCBI taxonomy identifier.
Selected viruses with medical relevance are given T4 identifiers and are part of the GENOME database. A new category of the GENES database, "vp" for virus mature peptides, has been introduced to define mature peptides cleaved from polyproteins for these selected viruses, which are often important to define protein interaction networks in KEGG pathway maps for viral infections.
Selected viruses with medical relevance are given T4 identifiers and are part of the GENOME database. A new category of the GENES database, "vp" for virus mature peptides, has been introduced to define mature peptides cleaved from polyproteins for these selected viruses, which are often important to define protein interaction networks in KEGG pathway maps for viral infections.
| Example | KEGG identifier | Remark |
| SARS-CoV-2 | T40361 | TAX:2697049 |
| SARS-CoV-2 S (spike) protein | vg:43740568 | K24152 |
| SARS-CoV-2 S1 (attachment) peptide | vp:43740568-1 | K25001 |
| SARS-CoV-2 S2 (fusion) peptide | vp:43740568-2 | K25002 |
Virus taxonomy
All the viruses present in KEGG GENES are classified according to the NCBI taxonomy, which is based on the ICTV (International Committee on Taxonomy of Viruses) classification, supplemented by KEGG with the traditional Baltimore classification (see br08620). The correspondence between the ICTV realm, kingdom, phylum, class, order, family classification and the seven types of Baltimore classification is shown below.
Riboviria
Pararnavirae
Artverviricota
Revtraviricetes
Blubervirales (VII dsDNA-RT)
Ortervirales (VI ssRNA-RT)
Caulimoviridae (VII dsDNA-RT)
Orthornavirae
Duplornaviricota (III dsRNA)
Pisuviricota
Duplopiviricetes (III dsRNA)
Durnavirales
Hypoviridae (IV +ssRNA)
Pisoniviricetes (IV +ssRNA)
Stelpaviricetes (IV +ssRNA)
Kitrinoviricota (IV +ssRNA)
Lenarviricota (IV +ssRNA)
Negarnaviricota (V -ssRNA)
Ribozyviria (V -ssRNA)
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Duplodnaviria (I dsDNA)
Varidnaviria (I dsDNA)
Adnaviria (I dsDNA)
Monodnaviria (II ssDNA)
Shotokuvirae
Cossaviricota
Papovaviricetes (I dsDNA)
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Last updated: June 18, 2021