virion — VIRION vertebrate-virus associations (2026)

Description

The Global Virome in One Network (VIRION), an atlas of the known associations between vertebrate hosts and their viruses, maintained by the Verena consortium (C. J. Carlson and collaborators). VIRION reconciles static datasets compiled from the literature (CLOVER, which harmonizes the host-pathogen databases of Shaw et al. 2020, HP3 of Olival et al. 2017, GMPD2 of Stephens et al. 2017 and EID2 of Wardeh et al. 2015) with dynamically updated sources (the virus sequences of NCBI GenBank and the USAID PREDICT surveillance data), and harmonizes all host and virus names against the NCBI taxonomy (and the ICTV taxonomy for viruses). This is the data package of 13 October 2026 (the database is released weekly). Two of the sources are also separate entries: mammal_virus_hp3 (HP3) and host_pathogen_eid2 (EID2, which covers all kinds of pathogens).

The network is bipartite and undirected: nodes are the taxa of the VIRION taxonomy table (vertebrate hosts, marked by the property is_host, and viruses), and each edge is one record of the database, i.e. one piece of evidence that a virus infects a host (e.g. a GenBank sequence, a literature report, or a PREDICT test), so that the network is a multigraph: a host and a virus are connected by as many edges as there are records of their association. Nodes are identified by the taxon key of the database (tax_hash), not by the name: some names occur in several taxon entries with different taxonomic information (e.g. NCBI-resolved or not). The NCBI accession numbers of the sequences (a separate table of the data package) are not included. A few records (1,069) are encoded in Latin-1 instead of UTF-8, which were converted.

The network has the following properties:

(Node) name: the scientific name of the taxon (in lower case, as in the database).
(Node) is_host: whether the node is a host (otherwise a virus).
(Node) genus, family, order, class: the taxonomy of the taxon (empty if not available).
(Node) ncbi_taxid: the NCBI taxonomy identifier (-1 if not available).
(Node) ncbi_resolved: whether the name could be harmonized with the NCBI taxonomy.
(Node) ictv_ratified: whether the virus taxon is ratified by the ICTV (false for hosts).
(Node) tax_hash: the key of the taxon in the database.
(Edge) detection_method: the strength of the evidence, one of "Isolation/Observation", "PCR/Sequencing", "Antibodies" and "Not specified", in descending order of strength.
(Edge) detection_original: the detection method as described in the source.
(Edge) database: the source of the record (GenBank, PREDICT, Shaw, HP3, GMPD2 or EID2), and database_version, its version or citation.
(Edge) host_original and virus_original: the names of the host and the virus in the source.
(Edge) host_flag: whether there is possible uncertainty in the identification of the host.
(Edge) publication_year: the year of publication of the literature source (NaN if not given); reference, its text description, and pmid, its PubMed identifier (empty if not given).
(Edge) release_date: the date the association was released to the public (e.g. the GenBank submission), as "YYYY-MM-DD" or partial ("YYYY", "YYYY-MM"), empty if not given.
(Edge) collection_date: the date of collection of the sample, as given (mostly "YYYY-MM-DD" or partial dates; empty if not given).
(Edge) assoc_id: the identifier of the record in this version of the database.

Tags

Biological Public Health Unweighted Multigraph Metadata

Added

2026-10-27

Citation

C. J. Carlson, R. J. Gibb, G. F. Albery, L. Brierley, R. P. Connor, T. A. Dallas, et al., "The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations." mBio 13(2), e02985-21 (2022) 10.1128/mbio.02985-21 Sci-Hub

Upstream URL OK

https://zenodo.org/records/23345630
https://github.com/viralemergence/virion

Upstream license

Open Data Commons Open Database License (ODbL), https://opendatacommons.org/licenses/odbl/

Networks

Tip: hover over a column header 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
virion	15,848	904,234	114.11	5639.45	36.39	153.31	-0.32	0.00	15	0.90	Undirected	Bipartite	name genus family order class ncbi_taxid ncbi_resolved ictv_ratified tax_hash is_host	detection_method detection_original database database_version host_original virus_original host_flag publication_year reference pmid release_date collection_date assoc_id	4.1 MiB	9.1 MiB	8.9 MiB	8.2 MiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.