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Blagrove_et_al_2022_poxvriuses data and code

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Version 2 2022-12-22, 19:38
Version 1 2022-08-13, 15:40
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posted on 2022-08-13, 15:40 authored by Maya WardehMaya Wardeh

Data and code for: "Monkeypox virus shows potential to infect a diverse range of native animal species across Europe, indicating high risk of becoming endemic in the region."

Authors:

Marcus SC Blagrove*1, Jack Pilgrim1, Aurelia Kotsiri1, Melody Hui1, Matthew Baylis1, Maya Wardeh*1,2

* = corresponding authors

1) Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK

2) Department of Mathematical Sciences, University of Liverpool, Liverpool, UK


Abstract:

Background: Monkeypox is a zoonotic virus which persists in animal reservoirs and periodically spills over into humans, causing outbreaks. During the current 2022 outbreak, monkeypox virus has persisted via human-human transmission, across all major continents and for longer than any previous record. This unprecedented spread creates the potential for the virus to ‘spillback’ into local susceptible animal populations. Persistent transmission amongst such animals raises the prospect of monkeypox virus becoming enzootic in new regions. However, the full and specific range of potential animal hosts and reservoirs of monkeypox remains unknown, especially in newly at-risk non-endemic areas. 


Methods: Here, our pipeline utilises ensembles of classifiers comprising different class balancing techniques and incorporating instance weights, to identify which animal species are potentially susceptible to monkeypox virus. Subsequently, we generate spatial distribution maps to highlight high-risk geographic areas at high resolution.


Findings: We show that the number of potentially susceptible species is currently underestimated by 2.4 to 4.3-fold. We show a high density of susceptible wild hosts in Europe. We provide lists of these species, and highlight high-risk hosts for spillback and potential long-term reservoirs, which may enable monkeypox virus to become endemic.


Funding

Global trade of coronavirus hosts: bringing geographically isolated hosts and viruses together risks novel recombination and spillover to humans

Biotechnology and Biological Sciences Research Council

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Where coronaviruses hide, where novel strains are generated, and how they get to us: Predicting reservoirs, recombination, and geographical hotspots

Natural Environment Research Council

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