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B."],"published-print":{"date-parts":[[2019,10,9]]},"abstract":"<jats:p>Variation in disease incidence in wildlife is often assumed to reflect environmental or demographic changes acting on an endemic pathogen. However, apparent endemicity might instead arise from spatial processes that are challenging to identify from traditional data sources including time series and field studies. Here, we analysed longitudinal sequence data collected from rabies virus outbreaks over 14 years in Costa Rica, a Central American country that has recorded continuous vampire bat-transmitted rabies outbreaks in humans and livestock since 1985. We identified five phylogenetically distinct lineages which shared most recent common ancestors with viruses from North and South America. Bayesian phylogeographic reconstructions supported bidirectional viral dispersals involving countries to the north and south of Costa Rica at different time points. Within Costa Rica, viruses showed little contemporaneous spatial overlap and no lineage was detected across all years of surveillance. Statistical models suggested that lineage disappearances were more likely to be explained by viral extinctions than undetected viral circulation. Our results highlight the importance of international viral dispersal for shaping the burden of rabies in Costa Rica, suggest a Central American corridor of rabies virus invasions between continents, and show that apparent disease endemicity may arise through recurrent pathogen extinctions and reinvasions which can be readily detected in relatively small datasets by joining phylodynamic and modelling approaches.<\/jats:p>","DOI":"10.1098\/rspb.2019.1527","type":"journal-article","created":{"date-parts":[[2019,10,9]],"date-time":"2019-10-09T07:06:18Z","timestamp":1570604778000},"page":"20191527","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":26,"title":["Phylodynamics reveals extinction\u2013recolonization dynamics underpin apparently endemic vampire bat rabies in Costa Rica"],"prefix":"10.1098","volume":"286","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7475-2705","authenticated-orcid":true,"given":"Daniel G.","family":"Streicker","sequence":"first","affiliation":[{"name":"MRC\u2014University of Glasgow Centre for Virus Research, Glasgow, UK"},{"name":"Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia Lucia","family":"Fallas Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Laboratorio de Pruebas de Paternidad, Caja Costarricense del Seguro Social, San Jos\u00e9, Costa Rica"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giovanna","family":"Luconi","sequence":"additional","affiliation":[{"name":"Cl\u00ednica Veterinaria Clivet, San Jos\u00e9, Costa Rica"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roc\u00edo Gonz\u00e1lez","family":"Barrientos","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioseguridad, Laboratorio Nacional de Servicios Veterinarios, Servicio Nacional de Salud Animal, Heredia, Costa Rica"},{"name":"Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernal","family":"Leon","sequence":"additional","affiliation":[{"name":"Laboratorio de Bioseguridad, Laboratorio Nacional de Servicios Veterinarios, Servicio Nacional de Salud Animal, Heredia, Costa Rica"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"175","published-online":{"date-parts":[[2019,10,9]]},"reference":[{"key":"e_1_3_6_2_2","doi-asserted-by":"publisher","DOI":"10.1080\/10408410701647560"},{"key":"e_1_3_6_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro.2017.45"},{"key":"e_1_3_6_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2014.03.002"},{"key":"e_1_3_6_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004796"},{"key":"e_1_3_6_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/ele.12428"},{"key":"e_1_3_6_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41559-018-0636-x"},{"key":"e_1_3_6_8_2","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.2003.68.191"},{"key":"e_1_3_6_9_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid2106.150123"},{"key":"e_1_3_6_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0914111107"},{"key":"e_1_3_6_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2005.07.004"},{"key":"e_1_3_6_12_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1461-0248.2005.00760.x"},{"key":"e_1_3_6_13_2","doi-asserted-by":"publisher","DOI":"10.1590\/S1020-49892009000300010"},{"key":"e_1_3_6_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virusres.2005.03.006"},{"key":"e_1_3_6_15_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0006105"},{"key":"e_1_3_6_16_2","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.12007"},{"key":"e_1_3_6_17_2","doi-asserted-by":"publisher","DOI":"10.1089\/vbz.2012.1113"},{"key":"e_1_3_6_18_2","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12728"},{"key":"e_1_3_6_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1606587113"},{"key":"e_1_3_6_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.44.5.1697-1710.2006"},{"key":"e_1_3_6_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1308817110"},{"key":"e_1_3_6_22_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2012.0538"},{"key":"e_1_3_6_23_2","first-page":"189","article-title":"Observations on the epizootiology of vampire bat rabies","volume":"9","author":"Lord RD","year":"1975","journal-title":"Bull. 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