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dc.contributor.authorO’Hare, Anthonyen_UK
dc.contributor.authorBalaz, Danielen_UK
dc.contributor.authorWright, David Men_UK
dc.contributor.authorMcCormick, Carlen_UK
dc.contributor.authorMcDowell, Stanleyen_UK
dc.contributor.authorTrewby, Hannahen_UK
dc.contributor.authorSkuce, Robin Aen_UK
dc.contributor.authorKao, Rowland Ren_UK
dc.description.abstractMulti-host pathogens are particularly difficult to control, especially when at least one of the hosts acts as a hidden reservoir. Deep sequencing of densely sampled pathogens has the potential to transform this understanding, but requires analytical approaches that jointly consider epidemiological and genetic data to best address this problem. While there has been considerable success in analyses of single species systems, the hidden reservoir problem is relatively under-studied. A well-known exemplar of this problem is bovine Tuberculosis, a disease found in British and Irish cattle caused by Mycobacterium bovis, where the Eurasian badger has long been believed to act as a reservoir but remains of poorly quantified importance except in very specific locations. As a result, the effort that should be directed at controlling disease in badgers is unclear. Here, we analyse densely collected epidemiological and genetic data from a cattle population but do not explicitly consider any data from badgers. We use a simulation modelling approach to show that, in our system, a model that exploits available cattle demographic and herd-to-herd movement data, but only considers the ability of a hidden reservoir to generate pathogen diversity, can be used to choose between different epidemiological scenarios. In our analysis, a model where the reservoir does not generate any diversity but contributes to new infections at a local farm scale are significantly preferred over models which generate diversity and/or spread disease at broader spatial scales. While we cannot directly attribute the role of the reservoir to badgers based on this analysis alone, the result supports the hypothesis that under current cattle control regimes, infected cattle alone cannot sustain M. bovis circulation. Given the observed close phylogenetic relationship for the bacteria taken from cattle and badgers sampled near to each other, the most parsimonious hypothesis is that the reservoir is the infected badger population. More broadly, our approach demonstrates that carefully constructed bespoke models can exploit the combination of genetic and epidemiological data to overcome issues of extreme data bias, and uncover important general characteristics of transmission in multi-host pathogen systems.en_UK
dc.publisherPublic Library of Science (PLoS)en_UK
dc.relationO’Hare A, Balaz D, Wright DM, McCormick C, McDowell S, Trewby H, Skuce RA & Kao RR (2021) A new phylodynamic model of Mycobacterium bovis transmission in a multi-host system uncovers the role of the unobserved reservoir. <i>PLOS Computational Biology</i>, 17 (6), Art. No.: e1009005.
dc.rights© 2021 O’Hare et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en_UK
dc.subjectModelling and Simulationen_UK
dc.subjectComputational Theory and Mathematicsen_UK
dc.subjectEcology, Evolution, Behavior and Systematicsen_UK
dc.subjectMolecular Biologyen_UK
dc.subjectCellular and Molecular Neuroscienceen_UK
dc.titleA new phylodynamic model of Mycobacterium bovis transmission in a multi-host system uncovers the role of the unobserved reservoiren_UK
dc.typeJournal Articleen_UK
dc.citation.jtitlePLoS Computational Biologyen_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderDepartment for Environment Food & Rural Affairsen_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.contributor.funderThe Wellcome Trusten_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
dc.contributor.affiliationQueen's University Belfasten_UK
dc.contributor.affiliationAgri-food & Biosciences Instituteen_UK
dc.contributor.affiliationAgri-food & Biosciences Instituteen_UK
dc.contributor.affiliationQuadram Instituteen_UK
dc.contributor.affiliationAgri-food & Biosciences Instituteen_UK
dc.contributor.affiliationUniversity of Edinburghen_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
local.rioxx.authorO’Hare, Anthony|0000-0003-2561-9582en_UK
local.rioxx.authorBalaz, Daniel|0000-0003-3958-8748en_UK
local.rioxx.authorWright, David M|0000-0001-8948-3691en_UK
local.rioxx.authorMcCormick, Carl|en_UK
local.rioxx.authorMcDowell, Stanley|en_UK
local.rioxx.authorTrewby, Hannah|0000-0001-8109-8107en_UK
local.rioxx.authorSkuce, Robin A|en_UK
local.rioxx.authorKao, Rowland R|0000-0003-0919-6401en_UK
local.rioxx.projectProject ID unknown|Biotechnology and Biological Sciences Research Council|
local.rioxx.projectProject ID unknown|The Wellcome Trust|en_UK
local.rioxx.projectProject ID unknown|Department for Environment Food & Rural Affairs|en_UK
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