KEGG Virus Resource

KEGG Virus is a resource for integrating viruses and cellular organisms from an evolutionary perspective. Virus data are part of the GENES, KO, GENOME, BRITE, PATHWAY, NETWORK, DISEASE and DRUG databases as summarized below.


Virus genes, proteins and KOs

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. Based on experimental evidence an increasing number of virus specific KOs are being defined. A new category of the GENES database, "vp" for virus mature peptides, has been introduced to define mature peptides cleaved from polyproteins for selected viruses, which are often important for defining protein interaction networks.
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

Selectee virus genomes

Selected viruses with relevance to human diseases or plant diseases are given T4 identifiers and are part of the GENOME database. Note that each T4 entry is a collection of virus genomes with the same taxonomy ID. Note also that T40000 is not part of KEGG GENOME; it simply represents the virus category of KEGG GENES.

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)
 Duplodnaviria       (I dsDNA)
 
 Varidnaviria        (I dsDNA)
 
 Adnaviria           (I dsDNA)
 
 Monodnaviria        (II ssDNA) 
   Shotokuvirae
     Cossaviricota
       Papovaviricetes (I dsDNA)

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 in taxonomic groups (family, genus species only)
Virus-cell interaction 03220 Virus entry
03222 Virus entry: animal viruses
Disease 08401 Infectious diseases (contains viral infections)
Drug 08307 Antimicrobials (contains antivirals and targets)
Comparison with
cellular organsms
01611 RNA polymerase
01612 DNA polymerase

Pathways and networks 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 is being expanded.

Category Pathway map Network variation map
Viral infections 05166 Human T-cell leukemia virus 1 infection 06160 HTLV-1
05170 Human immunodeficiency virus 1 infection 06161 HIV-1
05161 Hepatitis B 06162 HBV
05160 Hepatitis C 06163 HCV
05171 Coronavirus disease - COVID-19 06171 SARS-CoV-2
05164 Influenza A 06170 IAV
05162 Measles 06169 MV
05168 Herpes simplex virus 1 infection 06168 HSV-1
05163 Human cytomegalovirus infection 06167 HCMV
05167 Kaposi sarcoma-associated herpesvirus infection 06164 KSHV
05169 Epstein-Barr virus infection 06165 EBV
05165 Human papillomavirus infection 06166 HPV
05203 Viral carcinogenesis
Genetic information
processing in viruses
03230 Viral genome structure
03240 Viral replication
Comparison with
cellular organsms
03240 RNA polymerase


Last updated: June 22, 2022