{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T04:14:10Z","timestamp":1747196050148,"version":"3.40.5"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Universidade Eduardo Mondlane"},{"DOI":"10.13039\/501100009550","name":"Hasselt University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100009550","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Vlaamse Interuniversitaire Raad (VLIR-UOS) DESAFIO Program"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>A major outbreak of the Ebola virus occurred in 2014 in Sierra Leone. We investigate the spatial heterogeneity of the outbreak among districts in Sierra Leone. The stochastic discrete-time susceptible-exposed-infectious-removed (SEIR) model is used, allowing for probabilistic movements from one compartment to another. Our model accounts for heterogeneity among districts by making use of a hierarchical approach. The transmission rates are considered time-varying. It is investigated whether or not incubation period, infectious period and transmission rates are different among districts. Estimation is done using the Bayesian formalism. The posterior estimates of the effective reproductive number were substantially different across the districts, with pronounced variability in districts with few cases of Ebola. The posterior estimates of the reproductive number at the district level varied between below 1.0 and 4.5, whereas at nationwide level it varied between below 1.0 and 2.5. The posterior estimate of the effective reproductive number reached a value below 1.0 around December. In some districts, the effective reproductive number pointed out for the persistence of the outbreak or for a likely resurgence of new cases of Ebola virus disease (EVD). The posterior estimates have shown to be highly sensitive to prior elicitation, mainly the incubation period and infectious period.<\/jats:p>","DOI":"10.1371\/journal.pone.0250765","type":"journal-article","created":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T17:41:28Z","timestamp":1620927688000},"page":"e0250765","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-population stochastic modeling of Ebola in Sierra Leone: Investigation of spatial heterogeneity"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8721-085X","authenticated-orcid":true,"given":"Rachid","family":"Muleia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc","family":"Aerts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christel","family":"Faes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,5,13]]},"reference":[{"key":"pone.0250765.ref001","unstructured":"World Health Organization. Ebola Situation Report. 2015 June 24. [Cited 2015 August 22]. Available from: http:\/\/apps.who.int\/ebola\/current-situation\/ebola-situation-report-24-june-2015."},{"issue":"1","key":"pone.0250765.ref002","doi-asserted-by":"crossref","first-page":"11","DOI":"10.7326\/M14-2255","article-title":"Effect of Ebola Progression on Transmission and Control in Liberia","volume":"162","author":"D Yamin","year":"2015","journal-title":"Ann Intern Med"},{"key":"pone.0250765.ref003","first-page":"3","volume-title":"Advances in Ebola Control","author":"KK Aurelie","year":"2018"},{"key":"pone.0250765.ref004","unstructured":"World Health Organization. Statement on the 1st meeting of the IHR Emergency Committee on the 2014 Ebola outbreak in West Africa. 2014. [2015 August 25]. Available from: http:\/\/www.who.int\/mediacentre\/news\/statements\/2014\/ebola-20140808\/en\/."},{"key":"pone.0250765.ref005","unstructured":"Sierra Leone Ministry of Health and Sanitation. 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