references.bib

@article{Albery2020PreGlo,
  title = {Predicting the Global Mammalian Viral Sharing Network Using Phylogeography},
  author = {Albery, Gregory F. and Eskew, Evan A. and Ross, Noam and Olival, Kevin J.},
  year = {2020},
  month = may,
  volume = {11},
  pages = {2260},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-020-16153-4},
  abstract = {Understanding interspecific viral transmission is key to understanding viral ecology and evolution, disease spillover into humans, and the consequences of global change. Prior studies have uncovered macroecological drivers of viral sharing, but analyses have never attempted to predict viral sharing in a pan-mammalian context. Using a conservative modelling framework, we confirm that host phylogenetic similarity and geographic range overlap are strong, nonlinear predictors of viral sharing among species across the entire mammal class. Using these traits, we predict global viral sharing patterns of 4196 mammal species and show that our simulated network successfully predicts viral sharing and reservoir host status using internal validation and an external dataset. We predict high rates of mammalian viral sharing in the tropics, particularly among rodents and bats, and within- and between-order sharing differed geographically and taxonomically. Our results emphasize the importance of ecological and phylogenetic factors in shaping mammalian viral communities, and provide a robust, general model to predict viral host range and guide pathogen surveillance and conservation efforts.},
  copyright = {2020 The Author(s)},
  file = {/home/tpoisot/Zotero/storage/5S7S7WZA/Albery et al. - 2020 - Predicting the global mammalian viral sharing netw.pdf;/home/tpoisot/Zotero/storage/9LR29PEN/s41467-020-16153-4.html},
  journal = {Nature Communications},
  language = {en},
  number = {1}
}

@article{Banyard2017ImpNov,
  title = {The Impact of Novel Lyssavirus Discovery},
  author = {Banyard, Ashley C. and Fooks, Anthony R.},
  year = {2017},
  volume = {38},
  pages = {17--21},
  publisher = {{CSIRO}},
  file = {/home/tpoisot/Zotero/storage/M2J2FJ7R/Banyard and Fooks - 2017 - The impact of novel lyssavirus discovery.pdf;/home/tpoisot/Zotero/storage/F5WQ55TU/MA17006.html},
  journal = {Microbiology Australia},
  number = {1}
}

@article{Becker2020PreWil,
  title = {Predicting Wildlife Hosts of Betacoronaviruses for {{SARS}}-{{CoV}}-2 Sampling Prioritization},
  author = {Becker, Daniel J. and Albery, Gregory F. and Sjodin, Anna R. and Poisot, Timoth{\'e}e and Dallas, Tad A. and Eskew, Evan A. and Farrell, Maxwell J. and Guth, Sarah and Han, Barbara A. and Simmons, Nancy B. and Carlson, Colin J.},
  year = {2020},
  month = may,
  pages = {2020.05.22.111344},
  publisher = {{Cold Spring Harbor Laboratory}},
  doi = {10.1101/2020.05.22.111344},
  abstract = {{$<$}p{$>$}Despite massive investment in research on reservoirs of emerging pathogens, it remains difficult to rapidly identify the wildlife origins of novel zoonotic viruses. Viral surveillance is costly but rarely optimized using model-guided prioritization strategies, and predictions from a single model may be highly uncertain. Here, we generate an ensemble of seven network- and trait-based statistical models that predict mammal-virus associations, and we use model predictions to develop a set of priority recommendations for sampling potential bat reservoirs and intermediate hosts for SARS-CoV-2 and related betacoronaviruses. We find nearly 300 bat species globally could be undetected hosts of betacoronaviruses. Although over a dozen species of Asian horseshoe bats (Rhinolophus spp.) are known to harbor SARS-like viruses, we find at least two thirds of betacoronavirus reservoirs in this bat genus might still be undetected. Although identification of other probable mammal reservoirs is likely beyond existing predictive capacity, some of our findings are surprisingly plausible; for example, several civet and pangolin species were highlighted as high-priority species for viral sampling. Our results should not be over-interpreted as novel information about the plausibility or likelihood of SARS-CoV-29s ultimate origin, but rather these predictions could help guide sampling for novel potentially zoonotic viruses; immunological research to characterize key receptors (e.g., ACE2) and identify mechanisms of viral tolerance; and experimental infections to quantify competence of suspected host species.{$<$}/p{$>$}},
  chapter = {New Results},
  copyright = {\textcopyright{} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
  file = {/home/tpoisot/Zotero/storage/7F7UDU2J/Becker et al. - 2020 - Predicting wildlife hosts of betacoronaviruses for.pdf;/home/tpoisot/Zotero/storage/8BCLN42K/2020.05.22.html},
  journal = {bioRxiv},
  language = {en}
}

@article{Belaganahalli2015GenCha,
  ids = {Belaganahalli2015GenChaa},
  title = {Genetic {{Characterization}} of the {{Tick}}-{{Borne Orbiviruses}}},
  author = {Belaganahalli, Manjunatha N. and Maan, Sushila and Maan, Narender S. and Brownlie, Joe and Tesh, Robert and Attoui, Houssam and Mertens, Peter P. C.},
  year = {2015},
  month = apr,
  volume = {7},
  pages = {2185--2209},
  issn = {1999-4915},
  doi = {10.3390/v7052185},
  abstract = {The International Committee for Taxonomy of Viruses (ICTV) recognizes four species of tick-borne orbiviruses (TBOs): Chenuda virus, Chobar Gorge virus, Wad Medani virus and Great Island virus (genus Orbivirus, family Reoviridae). Nucleotide (nt) and amino acid (aa) sequence comparisons provide a basis for orbivirus detection and classification, however full genome sequence data were only available for the Great Island virus species. We report representative genome-sequences for the three other TBO species (virus isolates: Chenuda virus (CNUV); Chobar Gorge virus (CGV) and Wad Medani virus (WMV)). Phylogenetic comparisons show that TBOs cluster separately from insect-borne orbiviruses (IBOs). CNUV, CGV, WMV and GIV share low level aa/nt identities with other orbiviruses, in `conserved' Pol, T2 and T13 proteins/genes, identifying them as four distinct virus-species. The TBO genome segment encoding cell attachment, outer capsid protein 1 (OC1), is approximately half the size of the equivalent segment from insect-borne orbiviruses, helping to explain why tick-borne orbiviruses have a \textasciitilde 1 kb smaller genome.},
  file = {/home/tpoisot/Zotero/storage/9W77Q2PA/Belaganahalli et al. - 2015 - Genetic Characterization of the Tick-Borne Orbivir.pdf;/home/tpoisot/Zotero/storage/W4D54WSH/Belaganahalli et al. - 2015 - Genetic Characterization of the Tick-Borne Orbivir.pdf},
  journal = {Viruses},
  number = {5},
  pmcid = {PMC4452902},
  pmid = {25928203}
}

@article{Bezanson2017JulFre,
  title = {Julia: {{A Fresh Approach}} to {{Numerical Computing}}},
  shorttitle = {Julia},
  author = {Bezanson, J. and Edelman, A. and Karpinski, S. and Shah, V.},
  year = {2017},
  month = jan,
  volume = {59},
  pages = {65--98},
  issn = {0036-1445},
  doi = {10.1137/141000671},
  abstract = {Bridging cultures that have often been distant, Julia combines expertise from the diverse fields of computer science and computational science to create a new approach to numerical  computing. Julia is  designed to be easy and fast and questions notions generally held to be ``laws of nature"  by practitioners of numerical computing: \textbackslash beginlist \textbackslash item  High-level dynamic programs have to be slow. \textbackslash item  One must prototype in one language and then rewrite in another language for speed or deployment. \textbackslash item There are parts of a system appropriate for the programmer, and other parts that are best left untouched as they have been built by the experts. \textbackslash endlist We introduce the  Julia programming language and its design---a  dance between specialization and abstraction. Specialization allows for custom treatment. Multiple dispatch,  a  technique from computer science, picks  the right algorithm for the right circumstance. Abstraction, which is what good computation is really about, recognizes what remains the same after differences are stripped away. Abstractions in mathematics are captured as code through another technique from computer science, generic programming. Julia shows that  one can achieve machine performance without sacrificing human convenience.},
  file = {/home/tpoisot/Zotero/storage/CCSQEGV5/Bezanson et al. - 2017 - Julia A Fresh Approach to Numerical Computing.pdf;/home/tpoisot/Zotero/storage/N6I2YENF/141000671.html},
  journal = {SIAM Review},
  number = {1}
}

@article{Eckart1936AppOne,
  title = {The Approximation of One Matrix by Another of Lower Rank},
  author = {Eckart, Carl and Young, Gale},
  year = {1936},
  month = sep,
  volume = {1},
  pages = {211--218},
  issn = {1860-0980},
  doi = {10.1007/BF02288367},
  abstract = {The mathematical problem of approximating one matrix by another of lower rank is closely related to the fundamental postulate of factor-theory. When formulated as a least-squares problem, the normal equations cannot be immediately written down, since the elements of the approximate matrix are not independent of one another. The solution of the problem is simplified by first expressing the matrices in a canonic form. It is found that the problem always has a solution which is usually unique. Several conclusions can be drawn from the form of this solution.},
  journal = {Psychometrika},
  language = {en},
  number = {3}
}

@book{Forsythe1967ComSol,
  title = {Computer {{Solution}} of {{Linear Algebraic Systems}}},
  author = {Forsythe, George and Moler, Cleve},
  year = {1967},
  publisher = {{Prentice Hall}},
  address = {{Englewood Cliffs, New Jersey}}
}

@incollection{Golub1971SinVal,
  title = {Singular Value Decomposition and Least Squares Solutions},
  booktitle = {Linear {{Algebra}}},
  author = {Golub, Gene H. and Reinsch, Christian},
  year = {1971},
  pages = {134--151},
  publisher = {{Springer}}
}

@article{Golub1987GenEck,
  title = {A Generalization of the {{Eckart}}-{{Young}}-{{Mirsky}} Matrix Approximation Theorem},
  author = {Golub, G. H. and Hoffman, Alan and Stewart, G. W.},
  year = {1987},
  month = apr,
  volume = {88-89},
  pages = {317--327},
  issn = {0024-3795},
  doi = {10.1016/0024-3795(87)90114-5},
  abstract = {The Eckart-Young-Mirsky theorem solves the problem of approximating a matrix by one of lower rank. However, the approximation generally differs from the original in all its elements. In this paper it is shown how to obtain a best approximation of lower rank in which a specified set of columns of the matrix remains fixed. The paper concludes with some applications of the generalization.},
  file = {/home/tpoisot/Zotero/storage/C9XMJQCU/0024379587901145.html},
  journal = {Linear Algebra and its Applications},
  language = {en}
}

@article{Han2016FutDir,
  title = {Future Directions in Analytics for Infectious Disease Intelligence: {{Toward}} an Integrated Warning System for Emerging Pathogens},
  shorttitle = {Future Directions in Analytics for Infectious Disease Intelligence},
  author = {Han, Barbara A. and Drake, John M.},
  year = {2016},
  month = jun,
  volume = {17},
  pages = {785--789},
  issn = {1469-3178},
  doi = {10.15252/embr.201642534},
  file = {/home/tpoisot/Zotero/storage/W2AMCWKY/Han and Drake - 2016 - Future directions in analytics for infectious dise.pdf},
  journal = {EMBO reports},
  keywords = {Communicable Disease Control,Communicable Diseases; Emerging,Decision Support Systems; Clinical,Disease Outbreaks,Earthquakes,Global Warming,Humans,Risk,Tsunamis},
  language = {eng},
  number = {6},
  pmcid = {PMC5278609},
  pmid = {27170620}
}

@article{Hu2018LysJap,
  title = {Lyssavirus in {{Japanese Pipistrelle}}, {{Taiwan}} - {{Volume}} 24, {{Number}} 4\textemdash{{April}} 2018 - {{Emerging Infectious Diseases}} Journal - {{CDC}}},
  author = {Hu, Shu-Chia and Hsu, Chao-Lung and Lee, Ming-Shiuh and Tu, Yang-Chang and Chang, Jen-Chieh and Wu, Chieh-Hao and Lee, Shu-Hwae and Ting, Lu-Jen and Tsai, Kwok-Rong and Cheng, Ming-Chu and Tu, Wen-Jane and Hsu, Wei-Cheng},
  year = {2018},
  doi = {10.3201/eid2404.171696},
  abstract = {A putative new lyssavirus was found in 2 Japanese pipistrelles (Pipistrellus abramus) in Taiwan in 2016 and 2017. The concatenated coding regions of t...},
  file = {/home/tpoisot/Zotero/storage/786WMYUP/Hu et al. - Lyssavirus in Japanese Pipistrelle, Taiwan - Volum.pdf;/home/tpoisot/Zotero/storage/YCKD8WGF/17-1696_article.html},
  journal = {Emerging Infectious Diseases},
  language = {en-us}
}

@article{Johnson2020GloShi,
  title = {Global Shifts in Mammalian Population Trends Reveal Key Predictors of Virus Spillover Risk},
  author = {Johnson, Christine K. and Hitchens, Peta L. and Pandit, Pranav S. and Rushmore, Julie and Evans, Tierra Smiley and Young, Cristin C. W. and Doyle, Megan M.},
  year = {2020},
  month = apr,
  volume = {287},
  pages = {20192736},
  publisher = {{Royal Society}},
  doi = {10.1098/rspb.2019.2736},
  abstract = {Emerging infectious diseases in humans are frequently caused by pathogens originating from animal hosts, and zoonotic disease outbreaks present a major challenge to global health. To investigate drivers of virus spillover, we evaluated the number of viruses mammalian species have shared with humans. We discovered that the number of zoonotic viruses detected in mammalian species scales positively with global species abundance, suggesting that virus transmission risk has been highest from animal species that have increased in abundance and even expanded their range by adapting to human-dominated landscapes. Domesticated species, primates and bats were identified as having more zoonotic viruses than other species. Among threatened wildlife species, those with population reductions owing to exploitation and loss of habitat shared more viruses with humans. Exploitation of wildlife through hunting and trade facilitates close contact between wildlife and humans, and our findings provide further evidence that exploitation, as well as anthropogenic activities that have caused losses in wildlife habitat quality, have increased opportunities for animal\textendash human interactions and facilitated zoonotic disease transmission. Our study provides new evidence for assessing spillover risk from mammalian species and highlights convergent processes whereby the causes of wildlife population declines have facilitated the transmission of animal viruses to humans.},
  file = {/home/tpoisot/Zotero/storage/Y9VSZGQK/Johnson et al. - 2020 - Global shifts in mammalian population trends revea.pdf;/home/tpoisot/Zotero/storage/LCRG7R45/rspb.2019.html},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  number = {1924}
}

@article{Jones2008GloTre,
  title = {Global Trends in Emerging Infectious Diseases},
  author = {Jones, Kate E. and Patel, Nikkita G. and Levy, Marc A. and Storeygard, Adam and Balk, Deborah and Gittleman, John L. and Daszak, Peter},
  year = {2008},
  month = feb,
  volume = {451},
  pages = {990--993},
  publisher = {{Nature Publishing Group}},
  issn = {1476-4687},
  doi = {10.1038/nature06536},
  abstract = {Emerging infectious diseases are a major threat to health: AIDS, SARS, drug-resistant bacteria and Ebola virus are among the more recent examples. By identifying emerging disease 'hotspots', the thinking goes, it should be possible to spot health risks at an early stage and prepare containment strategies. An analysis of over 300 examples of disease emerging between 1940 and 2004 suggests that these hotspots can be accurately mapped based on socio-economic, environmental and ecological factors. The data show that the surveillance effort, and much current research spending, is concentrated in developed economies, yet the risk maps point to developing countries as the more likely source of new diseases.},
  copyright = {2008 Nature Publishing Group},
  file = {/home/tpoisot/Zotero/storage/JL5XIXVT/Jones et al. - 2008 - Global trends in emerging infectious diseases.pdf;/home/tpoisot/Zotero/storage/3J5T2CB6/nature06536.html},
  journal = {Nature},
  language = {en},
  number = {7181}
}

@article{Lloyd-Smith2009EpiDyn,
  title = {Epidemic {{Dynamics}} at the {{Human}}-{{Animal Interface}}},
  author = {{Lloyd-Smith}, James O. and George, Dylan and Pepin, Kim M. and Pitzer, Virginia E. and Pulliam, Juliet R. C. and Dobson, Andrew P. and Hudson, Peter J. and Grenfell, Bryan T.},
  year = {2009},
  month = dec,
  volume = {326},
  pages = {1362--1367},
  publisher = {{American Association for the Advancement of Science}},
  issn = {0036-8075, 1095-9203},
  doi = {10.1126/science.1177345},
  abstract = {Few infectious diseases are entirely human-specific: Most human pathogens also circulate in animals or else originated in nonhuman hosts. Influenza, plague, and trypanosomiasis are classic examples of zoonotic infections that transmit from animals to humans. The multihost ecology of zoonoses leads to complex dynamics, and analytical tools, such as mathematical modeling, are vital to the development of effective control policies and research agendas. Much attention has focused on modeling pathogens with simpler life cycles and immediate global urgency, such as influenza and severe acute respiratory syndrome. Meanwhile, vector-transmitted, chronic, and protozoan infections have been neglected, as have crucial processes such as cross-species transmission. Progress in understanding and combating zoonoses requires a new generation of models that addresses a broader set of pathogen life histories and integrates across host species and scientific disciplines.},
  chapter = {Review},
  copyright = {Copyright \textcopyright{} 2009, American Association for the Advancement of Science},
  file = {/home/tpoisot/Zotero/storage/552GA4F6/Lloyd-Smith et al. - 2009 - Epidemic Dynamics at the Human-Animal Interface.pdf;/home/tpoisot/Zotero/storage/GPM3CGHC/1362.html;/home/tpoisot/Zotero/storage/SBB6XVGC/1362.html},
  journal = {Science},
  language = {en},
  number = {5958},
  pmid = {19965751}
}

@article{Plowright2017PatZoo,
  title = {Pathways to Zoonotic Spillover},
  author = {Plowright, Raina K. and Parrish, Colin R. and McCallum, Hamish and Hudson, Peter J. and Ko, Albert I. and Graham, Andrea L. and {Lloyd-Smith}, James O.},
  year = {2017},
  month = aug,
  volume = {15},
  pages = {502--510},
  publisher = {{Nature Publishing Group}},
  issn = {1740-1534},
  doi = {10.1038/nrmicro.2017.45},
  abstract = {Zoonotic diseases present a substantial global health burden. In this Opinion article, Plowrightet al. present an integrative conceptual and quantitative model that reveals that all zoonotic pathogens must overcome a hierarchical series of barriers to cause spillover infections in humans.},
  copyright = {2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
  file = {/home/tpoisot/Zotero/storage/D9LI64UQ/Plowright et al. - 2017 - Pathways to zoonotic spillover.pdf;/home/tpoisot/Zotero/storage/PPYX9YRX/nrmicro.2017.html},
  journal = {Nature Reviews Microbiology},
  language = {en},
  number = {8}
}

@article{Pursell1972NatOcc,
  title = {Naturally Occurring and Artificially Induced Eastern Encephalomyelitis in Pigs},
  author = {Pursell, A. R. and Peckham, J. C. and Cole, J. R. and Stewart, W. C. and Mitchell, F. E.},
  year = {1972},
  month = nov,
  volume = {161},
  pages = {1143--1147},
  issn = {0003-1488},
  journal = {Journal of the American Veterinary Medical Association},
  keywords = {Animals,Brain,Cells; Cultured,Cytopathogenic Effect; Viral,Encephalitis Viruses,Encephalomyelitis; Equine,Kidney,Microscopy; Electron,Swine,Swine Diseases,Virus Cultivation},
  language = {eng},
  number = {10},
  pmid = {4652365}
}

@article{Ren2006FulGen,
  title = {Full-Length Genome Sequences of Two {{SARS}}-like Coronaviruses in Horseshoe Bats and Genetic Variation Analysis},
  author = {Ren, Wuze and Li, Wendong and Yu, Meng and Hao, Pei and Zhang, Yuan and Zhou, Peng and Zhang, Shuyi and Zhao, Guoping and Zhong, Yang and Wang, Shengyue and Wang, Lin-Fa and Shi, Zhengli},
  year = {2006},
  month = nov,
  volume = {87},
  pages = {3355--3359},
  issn = {0022-1317, 1465-2099},
  doi = {10.1099/vir.0.82220-0},
  abstract = {Bats were recently identified as natural reservoirs of SARS-like coronavirus (SL-CoV) or SARS coronavirus-like virus. These viruses, together with SARS coronaviruses (SARS-CoV) isolated from human and palm civet, form a distinctive cluster within the group 2 coronaviruses of the genus               Coronavirus               , tentatively named group 2b (G2b). In this study, complete genome sequences of two additional group 2b coronaviruses (G2b-CoVs) were determined from horseshoe bat               Rhinolophus ferrumequinum               (G2b-CoV Rf1) and               Rhinolophus macrotis               (G2b-CoV Rm1). The bat G2b-CoV isolates have an identical genome organization and share an overall genome sequence identity of 88\textendash 92{$\mkern1mu\%$} among themselves and between them and the human/civet isolates. The most variable regions are located in the genes encoding nsp3, ORF3a, spike protein and ORF8 when bat and human/civet G2b-CoV isolates are compared. Genetic analysis demonstrated that a diverse G2b-CoV population exists in the bat habitat and has evolved from a common ancestor of SARS-CoV.},
  file = {/home/tpoisot/Zotero/storage/IYMQNJJR/Ren et al. - 2006 - Full-length genome sequences of two SARS-like coro.pdf},
  journal = {Journal of General Virology},
  language = {en},
  number = {11}
}

@article{Sato2004GenPhy,
  title = {Genetic and {{Phylogenetic Analysis}} of {{Glycoprotein}} of {{Rabies Virus Isolated}} from {{Several Species}} in {{Brazil}}},
  author = {Sato, Go and Itou, Takuya and Shoji, Youko and Miura, Yasuo and Mikami, Takeshi and Ito, Mikako and Kurane, Ichiro and Samara, Samir I. and Carvalho, Adolorata A. B. and Nociti, Darci P. and Ito, Fumio H. and Sakai, Takeo},
  year = {2004},
  volume = {66},
  pages = {747--753},
  doi = {10.1292/jvms.66.747},
  abstract = {Genetic and phylogenetic analyses of the region containing the glycoprotein (G) gene, which is related to pathogenicity and antigenicity, and the G-L intergenic region were carried out in 14 Brazilian rabies virus isolates. The isolates were classified as dog-related rabies virus (DRRV) or vampire bat-related rabies virus (VRRV), by nucleoprotein (N) analysis. The nucleotide and amino acid (AA) homologies of the area containing the G protein gene and G-L intergenic region were generally lower than those of the ectodomain. In both regions, nucleotide and deduced AA homologies were lower among VRRVs than among DRRVs. There were AA differences between DRRV and VRRV at 3 antigenic sites and epitopes (IIa, WB+ and III), suggesting that DRRV and VRRV can be distinguished by differences of antigenicity. In a comparison of phylogenetic trees between the ectodomain and the area containing the G protein gene and G-L intergenic region, the branching patterns of the chiropteran and carnivoran rabies virus groups differed, whereas there were clear similarities in patterns within the DRRV and VRRV groups. Additionally, the VRRV isolates were more closely related to chiropteran strains isolated from Latin America than to Brazilian DRRV. These results indicate that Brazilian rabies virus isolates can be classified as DRRV or VRRV by analysis of the G gene and the G-L intergenic region, as well as by N gene analysis.},
  file = {/home/tpoisot/Zotero/storage/4VSH6TR7/Sato et al. - 2004 - Genetic and Phylogenetic Analysis of Glycoprotein .pdf;/home/tpoisot/Zotero/storage/D2743J69/_article.html},
  journal = {Journal of Veterinary Medical Science},
  keywords = {Brazil,glycoprotein,molecular epidemiology,rabies virus,vampire bat},
  number = {7}
}

@article{Shipley2019BatVir,
  title = {Bats and {{Viruses}}: {{Emergence}} of {{Novel Lyssaviruses}} and {{Association}} of {{Bats}} with {{Viral Zoonoses}} in the {{EU}}},
  shorttitle = {Bats and {{Viruses}}},
  author = {Shipley, Rebecca and Wright, Edward and Selden, David and Wu, Guanghui and Aegerter, James and Fooks, Anthony R and Banyard, Ashley C},
  year = {2019},
  month = feb,
  volume = {4},
  issn = {2414-6366},
  doi = {10.3390/tropicalmed4010031},
  abstract = {Bats in the EU have been associated with several zoonotic viral pathogens of significance to both human and animal health. Virus discovery continues to expand the existing understating of virus classification, and the increased interest in bats globally as reservoirs or carriers of zoonotic agents has fuelled the continued detection and characterisation of new lyssaviruses and other viral zoonoses. Although the transmission of lyssaviruses from bat species to humans or terrestrial species appears rare, interest in these viruses remains, through their ability to cause the invariably fatal encephalitis\textemdash rabies. The association of bats with other viral zoonoses is also of great interest. Much of the EU is free of terrestrial rabies, but several bat species harbor lyssaviruses that remain a risk to human and animal health. Whilst the rabies virus is the main cause of rabies globally, novel related viruses continue to be discovered, predominantly in bat populations, that are of interest purely through their classification within the lyssavirus genus alongside the rabies virus. Although the rabies virus is principally transmitted from the bite of infected dogs, these related lyssaviruses are primarily transmitted to humans and terrestrial carnivores by bats. Even though reports of zoonotic viruses from bats within the EU are rare, to protect human and animal health, it is important characterise novel bat viruses for several reasons, namely: (i) to investigate the mechanisms for the maintenance, potential routes of transmission, and resulting clinical signs, if any, in their natural hosts; (ii) to investigate the ability of existing vaccines, where available, to protect against these viruses; (iii) to evaluate the potential for spill over and onward transmission of viral pathogens in novel terrestrial hosts. This review is an update on the current situation regarding zoonotic virus discovery within bats in the EU, and provides details of potential future mechanisms to control the threat from these deadly pathogens.},
  file = {/home/tpoisot/Zotero/storage/QD4WXB8W/Shipley et al. - 2019 - Bats and Viruses Emergence of Novel Lyssaviruses .pdf},
  journal = {Tropical Medicine and Infectious Disease},
  number = {1},
  pmcid = {PMC6473451},
  pmid = {30736432}
}

@article{Stock2017LinFil,
  title = {Linear Filtering Reveals False Negatives in Species Interaction Data},
  author = {Stock, Michiel and Poisot, Timoth{\'e}e and Waegeman, Willem and Baets, Bernard De},
  year = {2017},
  month = apr,
  volume = {7},
  pages = {45908},
  issn = {2045-2322},
  doi = {10.1038/srep45908},
  abstract = {Species interaction datasets, often represented as sparse matrices, are usually collected through observation studies targeted at identifying species interactions.},
  copyright = {\textcopyright{} 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
  file = {/home/tpoisot/Zotero/storage/XQ4ANXCL/srep45908.html},
  journal = {Scientific Reports},
  language = {en}
}

@article{Wang2014RabRab,
  title = {Rabies and Rabies Virus in Wildlife in Mainland {{China}}, 1990\textendash 2013},
  author = {Wang, Lihua and Tang, Qing and Liang, Guodong},
  year = {2014},
  month = aug,
  volume = {25},
  pages = {122--129},
  issn = {1201-9712},
  doi = {10.1016/j.ijid.2014.04.016},
  abstract = {The number of wildlife rabies and wildlife-associated human and livestock rabies cases has increased in recent years, particularly in the southeast and northeast regions of mainland China. To better understand wildlife rabies and its role in human and livestock rabies, we reviewed what is known about wildlife rabies from the 1990s to 2013 in mainland China. In addition, the genetic diversity and phylogeny of available wildlife-originated rabies viruses (RABVs) were analyzed. Several wildlife species carry rabies including the bat, Chinese ferret badger, raccoon dog, rat, fox, and wolf. RABVs have been isolated or detected in the bat, Chinese ferret badger, raccoon dog, Apodemus, deer, and vole. Among them, the bat, Chinese ferret badger, and raccoon dog may play a role in the ecology of lyssaviruses in mainland China. All wildlife-originated RABVs were found to belong to genotype 1 RABV except for a bat-originated Irkut virus isolated in 2012. Several substitutions were found between the glycoprotein of wildlife-originated RABVs and vaccine strains. Whether these substitutions could affect the efficacy of currently used vaccines against infections caused by these wildlife-originated RABVs needs to be investigated further. Phylogenetic analysis showed that RABVs in the bat, Chinese ferret badger, and raccoon dog were distinct from local dog-originated RABVs, and almost all collected wildlife-originated isolates were associated with older China clades II to V, suggesting the possibility of wildlife reservoirs in mainland China through the ages.},
  file = {/home/tpoisot/Zotero/storage/8RAXKRC8/Wang et al. - 2014 - Rabies and rabies virus in wildlife in mainland Ch.pdf;/home/tpoisot/Zotero/storage/EC6RHEPB/S1201971214015124.html},
  journal = {International Journal of Infectious Diseases},
  keywords = {Genetic diversity,Mainland China,Phylogeny,Wildlife rabies},
  language = {en}
}

@article{Warrell2004RabOth,
  title = {Rabies and Other Lyssavirus Diseases},
  author = {Warrell, M. J. and Warrell, D. A.},
  year = {2004},
  month = mar,
  volume = {363},
  pages = {959--969},
  publisher = {{Elsevier}},
  issn = {0140-6736, 1474-547X},
  doi = {10.1016/S0140-6736(04)15792-9},
  abstract = {{$<$}h2{$>$}Summary{$<$}/h2{$><$}p{$>$}The full scale of the global burden of human rabies is unknown, owing to inadequate surveillance of this fatal disease. However, the terror of hydrophobia, a cardinal symptom of rabies encephalitis, is suffered by tens of thousands of people each year. The recent discovery of enzootic European bat lyssavirus infection in the UK is indicative of our expanding awareness of the Lyssavirus genus. The main mammalian vector species vary geographically, so the health problems created by the lyssaviruses and their management differ throughout the world. The methods by which these neurotropic viruses hijack neurophysiological mechanisms while evading immune surveillance is beginning to be unravelled by, for example, studies of molecular motor transport systems. Meanwhile, enormous challenges remain in the control of animal rabies and the provision of accessible, appropriate human prophylaxis worldwide.{$<$}/p{$>$}},
  file = {/home/tpoisot/Zotero/storage/3ECMUHCA/fulltext.html;/home/tpoisot/Zotero/storage/UVZWCLM3/fulltext.html},
  journal = {The Lancet},
  language = {English},
  number = {9413},
  pmid = {15043965}
}