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Data from: Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species

Citation

Wells, Konstans; Morand, Serge; Wardeh, Maya; Baylis, Matthew (2020), Data from: Distinct spread of DNA and RNA viruses among mammals amid prominent role of domestic species, Dryad, Dataset, https://doi.org/10.5061/dryad.p2ngf1vmg

Abstract

Aim: Emerging infectious diseases arising from pathogen spillover from mammals to humans comprise a substantial health threat. Tracing virus origin and predicting the most likely host species for future spillover events are major objectives in One Health disciplines.

We assessed patterns of virus sharing among a large diversity of mammals, including humans and domestic species.

Location: Global.

Time period: Current.

Major taxa studied: Mammals and associated viruses.

Methods: We used network centrality analysis and trait-based Bayesian hierarchical models to explore patterns of virus sharing among mammals. We analysed a global database that compiled the associations between 1,785 virus species and 725 mammalian host species as sourced from automatic screening of meta-data accompanying published nucleotide sequences between 1950 – 2019.

Results: We show that based on current evidence, domesticated mammals hold the most central positions in networks of known mammal-virus associations. Among entire host-virus networks, Carnivora and Chiroptera hold central positions for mainly sharing RNA viruses, while Ungulates hold central positions for sharing both RNA and DNA viruses with other host species. We revealed strong evidence that DNA viruses were phylogenetically more host specific than RNA viruses. RNA viruses exhibited low functional host specificity despite an overall tendency to infect phylogenetically related species, signifying high potential to shift across hosts with different ecological niches. The frequencies of sharing viruses among hosts and the proportion of zoonotic viruses in hosts were larger for RNA than DNA viruses.

Main conclusions: Acknowledging the role of domestic species in addition to host and virus traits in patterns of virus sharing is necessary to improve our understanding of virus spread and spillover in times of global change. Understanding multi-host virus sharing pathways adds focus to curtail disease spread.

Methods

Mammal-virus species interaction matrix

Compiled matrix of mammal-virus species-level interactions from the Enhanced Infectious Diseases Database (EID2, online accessible at https://eid2.liverpool.ac.uk/) in the version from May 2018. Virus species names are those from the NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/Taxonomy/). Mammal species synonyms and taxonomic orders were standardized using the taxonomy of Wilson and Reeder (2005), the online version of IUCN Red List and Integrated Taxonomic Information System, ITIS (accessed May 2018). Mammalian species are arranged in rows (n=725 species) and virus species in columns (n= 1,785 species). Mammalian species are considered to be host to a virus if at least four independent publications or one sequence meta-data reported an association between the host (or any of its subspecies) and the virus (or any of its subspecies or strains). Such association are noted with ‘1’ in the respective cells, the lack of sufficient evidence for an association between a mammalian and virus species are noted with ‘0’ in the respective cell.