mammal_virus_hp3 — Mammal-virus associations (2017)

Description

Bipartite network of mammal species and the viruses known to infect them, from the database of host-virus associations compiled by Olival et al. (the Host-Pathogen Phylogeny Project, HP3) to study which host and viral traits predict zoonotic spillover. The associations were collected from a systematic review of the published literature, for virus species recognized by the International Committee on Taxonomy of Viruses (ICTV), with host names harmonized to the IUCN taxonomy. The database contains 754 mammal species (including humans) and 586 virus species.

A node is either a mammal species or a virus species, and each edge is a host-virus association reported in a reference, annotated with the method used to detect the virus in the host. A few host-virus pairs are reported in more than one reference with different methods, and appear as parallel edges.

The network has the following properties:

All nodes: name, the species name (with underscores in place of spaces); is_host, whether the node is a mammal species (otherwise it is a virus); order, family, and genus, the taxonomic order, family, and genus of the host or virus.
Hosts: common_name, the English common name(s); wild_domestic, whether the species is wild or domestic according to the FAO (or "human"); marine_terrestrial, whether the species is marine or terrestrial; mass_grams, the average body mass in grams (NaN if unknown); redlist_status, the IUCN Red List status; citations, the number of Zoological Abstracts records for the species, and disease_citations, the number of such records that also match disease-related keywords (both are measures of research effort, -1 if unknown).
Viruses: nucleic_acid (DNA or RNA), strandedness (SS or DS), envelope (enveloped or non-enveloped), genome_length, the average genome length in nucleotides (NaN if unknown), vector_borne ("Y", "N", or "NA" if unknown), is_zoonotic, whether the virus has been detected both in humans and in other mammals, and is_zoonotic_stringent, the same but considering only detections by PCR or virus isolation.
Edges: detection_method, the method used to detect the virus in the host (e.g. antibodies, PCR, isolation); detection_quality, the strength of the evidence: 0 for serology, 1 for a viral neutralization test, and 2 for PCR or virus isolation (-1 if not given); host_status, whether the host in the reference was wild, domestic, captive, or human; and reference, the short reference (author and year) reporting the association.

Tags

Biological Unweighted Multigraph Metadata

Citation

K. J. Olival, P. R. Hosseini, C. Zambrana-Torrelio, N. Ross, T. L. Bogich, P. Daszak, "Host and viral traits predict zoonotic spillover from mammals." Nature 546, 646-650 (2017) 10.1038/nature22975 Sci-Hub
K. J. Olival, P. R. Hosseini, C. Zambrana-Torrelio, N. Ross, T. L. Bogich, P. Daszak, "Host and Viral Traits Predict Zoonotic Spillover from Mammals" (data and code), Zenodo (2017) 10.5281/zenodo.596810 Sci-Hub

Upstream URL OK

https://github.com/ecohealthalliance/HP3

Upstream license

MIT, https://github.com/ecohealthalliance/HP3/blob/master/LICENSE

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
mammal_virus_hp3	1,340	2,805	4.19	10.31	13.83	20.32	-0.15	0.00	10	0.98	Undirected	Bipartite	name is_host order family genus common_name wild_domestic marine_terrestrial mass_grams redlist_status citations disease_citations nucleic_acid strandedness envelope genome_length vector_borne is_zoonotic is_zoonotic_stringent	detection_method detection_quality host_status reference	57 KiB	73 KiB	72 KiB	66 KiB