Poisot, Timothée;
Ouellet, Marie-Andrée;
Mollentze, Nardus;
Farrell, Maxwell J;
Becker, Daniel J;
Brierley, Liam;
Albery, Gregory F;
... Carlson, Colin J; + view all
(2023)
Network embedding unveils the hidden interactions in the mammalian virome.
Patterns
, 4
(6)
, Article 100738. 10.1016/j.patter.2023.100738.
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Abstract
Predicting host-virus interactions is fundamentally a network science problem. We develop a method for bipartite network prediction that combines a recommender system (linear filtering) with an imputation algorithm based on low-rank graph embedding. We test this method by applying it to a global database of mammal-virus interactions and thus show that it makes biologically plausible predictions that are robust to data biases. We find that the mammalian virome is under-characterized anywhere in the world. We suggest that future virus discovery efforts could prioritize the Amazon Basin (for its unique coevolutionary assemblages) and sub-Saharan Africa (for its poorly characterized zoonotic reservoirs). Graph embedding of the imputed network improves predictions of human infection from viral genome features, providing a shortlist of priorities for laboratory studies and surveillance. Overall, our study indicates that the global structure of the mammal-virus network contains a large amount of information that is recoverable, and this provides new insights into fundamental biology and disease emergence.
| Type: | Article |
|---|---|
| Title: | Network embedding unveils the hidden interactions in the mammalian virome |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.patter.2023.100738 |
| Publisher version: | https://doi.org/10.1016/j.patter.2023.100738 |
| Language: | English |
| Additional information: | © 2023 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10205873 |
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