logo Netzschleuder network catalog, repository, and centrifuge

virus_host_db — Virus-Host DB virus-host associations (2016-2026)

Description

Networks of viruses and their hosts from the Virus-Host DB of GenomeNet (Kyoto University), which covers all the viruses with complete genomes in NCBI RefSeq and in GenBank (as listed in EBI Genomes), across all domains of life (viruses of bacteria, archaea, protists, fungi, plants and animals, including humans). The hosts are collected from the annotations of RefSeq and GenBank, UniProt and ViralZone, and from a manual curation of the literature. Each virus and each host is an NCBI taxon, and an edge links a virus to a host in which it was found.

Virus-Host DB is updated with every RefSeq release (about every two months), and its earlier releases are archived. There is one network for each archived release, named release_<N> by the number of its directory in the archive, which is the RefSeq release on which it is based, from release_75 (2016) to release_236 (RefSeq release 236, July 6, 2026); the RefSeq release and its date are given by the graph properties refseq_release and refseq_date. Releases 76, 97, 201, 223, 234 are missing from the archive, except that the directory 224 holds the data of RefSeq release 223. The directory 232 holds the same data as 233 (of RefSeq release 233), and the file of the directory 230 (RefSeq release 230, May 2, 2025) is empty: both are left out. The first release, release_75, has no KEGG identifiers, diseases, PubMed identifiers and evidence.

The viruses whose genomes come from environmental samples (metagenomes) have as host the root of the taxonomy (taxon 1, root), with the kind of sample (e.g. Soil, Marine, Organismal) as edge property: this node is kept, and it joins all these viruses. Some viruses are hosts of other viruses (e.g. satellite viruses and virophages), so that a few edges join two viruses, and the networks are not strictly bipartite. The viruses without any host given are isolated nodes. A virus and a host are joined by several edges if they are listed several times (e.g. with different kinds of samples).

The networks have the following properties:

  • tax_id: the NCBI taxonomy identifier of the virus or host.
  • is_virus: whether the node is a virus (otherwise it is only a host).
  • name: the name of the virus or host.
  • lineage: the taxonomic lineage of the virus or host, separated by ;.
  • refseq_ids: the RefSeq (or GenBank) accessions of the genome of the virus, separated by , (empty for hosts).
  • kegg_genome, kegg_disease, disease: the KEGG GENOME and KEGG DISEASE identifiers of the virus, and the diseases it causes (empty if none, and for hosts).
  • Edge pmids (from release_77): the PubMed identifiers of the articles on the association, separated by ,.
  • Edge evidence (from release_77): the sources of the host information (RefSeq, Literature, UniProt, NCBI Virus, ...), separated by ,.
  • Edge sample_type (from release_89): the kind of environmental sample of the genome, if the host is the root of the taxonomy.
  • Edge source_organism (from release_89): the taxonomy identifier of the organism of the sample, for organismal samples (-1 if not given).
  • refseq_release, refseq_date (graph): the RefSeq release on which the network is based, and its date (empty if not given).
Tags
Biological Ecological Unweighted Multigraph Metadata
Citation
  • T. Mihara, Y. Nishimura, Y. Shimizu, H. Nishiyama, G. Yoshikawa, H. Uehara, P. Hingamp, S. Goto, H. Ogata, "Linking Virus Genomes with Host Taxonomy." Viruses 8, 66 (2016) 10.3390/v8030066 Sci-Hub
Upstream URL OK
https://www.genome.jp/virushostdb/
https://www.genome.jp/ftp/db/virushostdb/
Upstream license
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0), https://creativecommons.org/licenses/by-nc-sa/4.0/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
release_75 10,350 9,772 1.89 11.75 8.62 10341.17 -0.11 0.00 29 0.42 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease 196 KiB 237 KiB 238 KiB 306 KiB
release_77 10,516 9,871 1.88 11.89 8.62 10457.56 -0.11 0.00 29 0.41 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 211 KiB 260 KiB 260 KiB 326 KiB
release_78 10,515 9,870 1.88 11.88 8.62 10452.87 -0.11 0.00 29 0.41 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 211 KiB 260 KiB 260 KiB 326 KiB
release_79 10,638 10,050 1.89 11.87 8.65 10766.79 -0.11 0.00 30 0.42 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 214 KiB 264 KiB 265 KiB 331 KiB
release_80 11,614 10,847 1.87 11.98 8.64 10955.15 -0.10 0.00 26 0.39 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 230 KiB 285 KiB 285 KiB 358 KiB
release_81 11,615 10,986 1.89 12.29 8.64 11177.06 -0.10 0.00 26 0.40 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 230 KiB 285 KiB 286 KiB 359 KiB
release_82 12,400 11,668 1.88 11.98 8.64 11306.93 -0.10 0.00 26 0.38 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 239 KiB 299 KiB 300 KiB 376 KiB
release_83 12,548 11,967 1.91 12.09 8.65 12595.64 -0.10 0.00 32 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 246 KiB 306 KiB 307 KiB 384 KiB
release_84 12,781 12,199 1.91 12.04 8.72 12855.75 -0.10 0.00 32 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 251 KiB 313 KiB 314 KiB 393 KiB
release_85 12,855 12,287 1.91 12.31 8.73 13055.75 -0.10 0.00 32 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 254 KiB 315 KiB 316 KiB 397 KiB
release_86 12,862 12,345 1.92 12.47 8.73 13226.79 -0.10 0.00 32 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 254 KiB 316 KiB 317 KiB 397 KiB
release_87 12,906 12,420 1.92 12.76 8.73 12334.20 -0.10 0.00 26 0.40 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 255 KiB 317 KiB 318 KiB 398 KiB
release_88 12,951 12,485 1.93 12.75 8.70 12346.16 -0.10 0.00 26 0.40 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence 256 KiB 319 KiB 320 KiB 400 KiB
release_89 12,903 12,501 1.94 16.45 8.70 15884.81 -0.15 0.00 26 0.47 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 255 KiB 321 KiB 323 KiB 402 KiB
release_90 13,562 13,896 2.05 16.59 9.40 1122.89 -0.14 0.00 23 0.51 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 269 KiB 341 KiB 343 KiB 426 KiB
release_91 13,605 14,550 2.14 16.81 18.43 1273.32 -0.14 0.00 22 0.49 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 274 KiB 349 KiB 351 KiB 433 KiB
release_92 13,582 14,099 2.08 16.72 17.70 3177.12 -0.14 0.00 25 0.48 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 273 KiB 346 KiB 347 KiB 431 KiB
release_93 14,056 14,113 2.01 16.30 12.67 5926.12 -0.14 0.00 24 0.47 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 283 KiB 357 KiB 360 KiB 449 KiB
release_94 14,297 14,227 1.99 16.24 14.24 4667.96 -0.14 0.00 24 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 287 KiB 364 KiB 366 KiB 449 KiB
release_95 14,738 14,625 1.98 16.12 15.50 4699.70 -0.14 0.00 23 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 297 KiB 374 KiB 378 KiB 463 KiB
release_96 14,740 14,637 1.99 16.14 15.50 4688.33 -0.14 0.00 23 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 297 KiB 375 KiB 377 KiB 463 KiB
release_98 14,802 14,501 1.96 15.97 8.97 4267.38 -0.13 0.00 23 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 300 KiB 377 KiB 379 KiB 466 KiB
release_99 14,810 14,512 1.96 15.97 8.97 4261.82 -0.13 0.00 23 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 300 KiB 377 KiB 380 KiB 466 KiB
release_200 14,828 14,520 1.96 15.95 8.97 4260.75 -0.13 0.00 23 0.46 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 300 KiB 378 KiB 381 KiB 467 KiB
release_202 15,990 15,958 2.00 15.77 9.46 4130.30 -0.13 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 334 KiB 424 KiB 428 KiB 552 KiB
release_203 15,999 16,046 2.01 15.99 9.54 4154.18 -0.13 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 335 KiB 425 KiB 429 KiB 553 KiB
release_204 16,182 16,273 2.01 16.23 9.73 3995.48 -0.14 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 338 KiB 430 KiB 434 KiB 559 KiB
release_205 16,360 16,614 2.03 16.51 10.08 4094.80 -0.14 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 342 KiB 436 KiB 441 KiB 566 KiB
release_206 16,592 16,924 2.04 16.72 10.10 3389.12 -0.14 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 347 KiB 443 KiB 447 KiB 573 KiB
release_207 17,423 17,547 2.01 16.16 10.46 3738.38 -0.14 0.00 32 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 367 KiB 468 KiB 473 KiB 605 KiB
release_208 17,427 17,730 2.03 16.79 10.77 3788.79 -0.14 0.00 32 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 371 KiB 473 KiB 477 KiB 610 KiB
release_209 17,455 17,823 2.04 16.90 10.85 3746.22 -0.14 0.00 32 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 373 KiB 474 KiB 478 KiB 612 KiB
release_210 17,482 17,864 2.04 16.95 10.80 4588.80 -0.14 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 375 KiB 476 KiB 480 KiB 614 KiB
release_211 17,536 18,000 2.05 17.16 11.03 3914.44 -0.14 0.00 28 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 378 KiB 480 KiB 484 KiB 618 KiB
release_212 17,564 18,123 2.06 17.21 11.37 3673.04 -0.14 0.00 26 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 381 KiB 483 KiB 488 KiB 621 KiB
release_213 17,485 18,087 2.07 17.28 11.70 3684.43 -0.14 0.00 24 0.45 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 383 KiB 485 KiB 490 KiB 623 KiB
release_214 17,291 17,899 2.07 17.36 11.68 2463.69 -0.14 0.00 24 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 384 KiB 485 KiB 488 KiB 620 KiB
release_215 17,315 17,958 2.07 17.36 11.71 2323.09 -0.14 0.00 24 0.44 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 385 KiB 485 KiB 489 KiB 621 KiB
release_216 17,254 17,860 2.07 17.51 11.90 6198.65 -0.14 0.00 27 0.50 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 384 KiB 484 KiB 489 KiB 619 KiB
release_217 17,747 18,406 2.07 17.37 11.93 6986.99 -0.14 0.00 27 0.49 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 391 KiB 496 KiB 499 KiB 631 KiB
release_218 18,887 18,663 1.98 16.76 11.91 8247.43 -0.14 0.00 25 0.47 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 409 KiB 518 KiB 523 KiB 660 KiB
release_219 20,574 20,838 2.03 20.74 12.07 8465.72 -0.13 0.00 25 0.50 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 452 KiB 572 KiB 577 KiB 736 KiB
release_220 20,594 21,012 2.04 20.80 12.39 7257.84 -0.13 0.00 25 0.50 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 453 KiB 575 KiB 580 KiB 739 KiB
release_221 33,481 33,337 1.99 20.97 12.44 17398.57 -0.16 0.00 27 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 620 KiB 807 KiB 825 KiB 1.0 MiB
release_222 33,471 33,283 1.99 21.39 12.44 18388.99 -0.16 0.00 27 0.41 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 621 KiB 807 KiB 825 KiB 1.0 MiB
release_224 33,478 33,490 2.00 21.97 12.44 20235.25 -0.15 0.00 27 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 623 KiB 811 KiB 829 KiB 1.0 MiB
release_225 33,502 33,506 2.00 22.63 12.60 19111.16 -0.15 0.00 27 0.43 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 628 KiB 814 KiB 833 KiB 1.0 MiB
release_226 36,317 36,312 2.00 23.00 12.73 8164.00 -0.16 0.00 27 0.26 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 663 KiB 866 KiB 887 KiB 1.1 MiB
release_227 38,031 36,994 1.95 23.07 12.78 5564.53 -0.16 0.00 27 0.26 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 674 KiB 885 KiB 910 KiB 1.1 MiB
release_228 38,358 37,879 1.98 23.98 12.75 5597.24 -0.16 0.00 27 0.26 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 680 KiB 894 KiB 918 KiB 1.1 MiB
release_229 39,789 39,319 1.98 24.35 12.84 5616.13 -0.17 0.00 27 0.25 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 690 KiB 911 KiB 937 KiB 1.2 MiB
release_231 40,695 39,945 1.96 25.11 12.79 9186.54 -0.17 0.00 29 0.25 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 727 KiB 953 KiB 978 KiB 1.2 MiB
release_233 42,415 42,169 1.99 25.82 12.76 6063.57 -0.16 0.00 29 0.27 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 754 KiB 994 KiB 1022 KiB 1.3 MiB
release_235 42,707 42,325 1.98 25.93 12.67 5177.30 -0.16 0.00 29 0.27 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 770 KiB 1009 KiB 1.0 MiB 1.3 MiB
release_236 42,904 42,632 1.99 26.53 12.68 6001.19 -0.16 0.00 30 0.28 Undirected Unipartite tax_id is_virus name lineage refseq_ids kegg_genome kegg_disease disease pmids evidence sample_type source_organism 775 KiB 1018 KiB 1.0 MiB 1.3 MiB