{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T23:25:39Z","timestamp":1790378739184,"version":"4.1.0"},"reference-count":53,"publisher":"The Royal Society","issue":"131","license":[{"start":{"date-parts":[[2017,6,1]],"date-time":"2017-06-01T00:00:00Z","timestamp":1496275200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/royalsociety.org\/journals\/ethics-policies\/data-sharing-mining\/"}],"funder":[{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["HPRU-2012-10080"],"award-info":[{"award-number":["HPRU-2012-10080"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","award":["HPRU-2012-10414"],"award-info":[{"award-number":["HPRU-2012-10414"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["J. R. Soc. Interface."],"published-print":{"date-parts":[[2017,6]]},"abstract":"<jats:p>\n                    Bubonic plague has caused three deadly pandemics in human history: from the mid-sixth to mid-eighth century, from the mid-fourteenth to the mid-eighteenth century and from the end of the nineteenth until the mid-twentieth century. Between the second and the third pandemics, plague was causing sporadic outbreaks in only a few countries in the Middle East, including Egypt. Little is known about this historical phase of plague, even though it represents the temporal, geographical and phylogenetic transition between the second and third pandemics. Here we analysed in detail an outbreak of plague that took place in Cairo in 1801, and for which epidemiological data are uniquely available thanks to the presence of medical officers accompanying the Napoleonic expedition into Egypt at that time. We propose a new stochastic model describing how bubonic plague outbreaks unfold in both rat and human populations, and perform Bayesian inference under this model using a particle Markov chain Monte Carlo. Rat carcasses were estimated to be infectious for approximately 4 days after death, which is in good agreement with local observations on the survival of infectious rat fleas. The estimated transmission rate between rats implies a basic reproduction number\n                    <jats:italic>R<\/jats:italic>\n                    <jats:sub>0<\/jats:sub>\n                    of approximately 3, causing the collapse of the rat population in approximately 100 days. Simultaneously, the force of infection exerted by each infected rat carcass onto the human population increases progressively by more than an order of magnitude. We also considered human-to-human transmission via pneumonic plague or human specific vectors, but found this route to account for only a small fraction of cases and to be significantly below the threshold required to sustain an outbreak.\n                  <\/jats:p>","DOI":"10.1098\/rsif.2017.0160","type":"journal-article","created":{"date-parts":[[2017,6,21]],"date-time":"2017-06-21T05:10:11Z","timestamp":1498021811000},"page":"20170160","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":18,"title":["Model-based analysis of an outbreak of bubonic plague in Cairo in 1801"],"prefix":"10.1098","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1885-500X","authenticated-orcid":false,"given":"Xavier","family":"Didelot","sequence":"first","affiliation":[{"name":"Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilith K.","family":"Whittles","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian","family":"Hall","sequence":"additional","affiliation":[{"name":"Bioterrorism and Emerging Disease Analysis, Emergency Response Department, Health Protection and Medical Directorate, Public Health England, Porton Down SP4 0JG, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"175","published-online":{"date-parts":[[2017,6,21]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.10.009"},{"key":"e_1_3_5_3_2","article-title":"The stone age plague: 1000 years of persistence in eurasia","author":"Valtuena AA","year":"2017","journal-title":"bioRxiv"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1413209111"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1421887112"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0022172400014558"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mehy.2007.02.036"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid0202.960219"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1286-4579(01)01515-5"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003349"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(13)70323-2"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF03208570"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/actrade\/9780199589548.001.0001"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.220225197"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature10549"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1205750110"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.11.016"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.1111\/ehr.12098"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2016.0618"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.10.1.35"},{"key":"e_1_3_5_21_2","volume-title":"The fertile crescent, 1800\u20131914: a documentary economic history","author":"Issawi C","year":"1988"},{"key":"e_1_3_5_22_2","doi-asserted-by":"crossref","first-page":"387","DOI":"10.3406\/adh.1981.1512","article-title":"Notes sur les \u00e9pid\u00e9mies de peste en Egypte","author":"Shoshan B","year":"1981","journal-title":"D\u00e9mographie Hist. Cond. f\u00e9minine"},{"key":"e_1_3_5_23_2","first-page":"203","article-title":"Les Grandes Epidemies de Peste au Caire aux XVII e et XVIII e Siecles","volume":"25","author":"Raymond A","year":"1972","journal-title":"Bull. d'\u00e9tudes Orient."},{"key":"e_1_3_5_24_2","first-page":"201","article-title":"La Population du Caire, de Maqrizi a la Description de L'Egypte","volume":"28","author":"Raymond A","year":"1975","journal-title":"Bull. d'\u00e9tudes Orient."},{"key":"e_1_3_5_25_2","doi-asserted-by":"publisher","DOI":"10.3406\/remmm.1987.2191"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1353\/bhm.0.0031"},{"key":"e_1_3_5_27_2","first-page":"162","article-title":"The second plague pandemic and its recurrences in the Middle East: 1347\u20131894","volume":"22","author":"Dols MW","year":"1979","journal-title":"J. Econ. Soc. Hist. Orient"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0022172400008548"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.327.7429.1461"},{"key":"e_1_3_5_30_2","first-page":"19","article-title":"La litt\u00e9rature m\u00e9dicale de la campagne d'\u00c9gypte","volume":"46","author":"Hutin J-F","year":"2012","journal-title":"Hist. Sci. Med."},{"key":"e_1_3_5_31_2","volume-title":"Histoire m\u00e9dicale de l'arm\u00e9e d'Orient","author":"Desgenettes R","year":"1802"},{"key":"e_1_3_5_32_2","volume-title":"M\u00e9moires sur les fi\u00e8vres pestilentielles et insidieuses du Levant","author":"Pugnet JFX","year":"1804"},{"key":"e_1_3_5_33_2","first-page":"454","volume-title":"Descr. l'Egypte","author":"Larrey DJ","year":"1809"},{"key":"e_1_3_5_34_2","volume-title":"Memoires de chirurgie militaire, et campagnes","author":"Larrey DJ","year":"1812"},{"key":"e_1_3_5_35_2","volume-title":"Histoire scientifique et militaire de l'exp\u00e9dition francaise en \u00c9gypte","author":"Reybaud L","year":"1832"},{"key":"e_1_3_5_36_2","first-page":"121","article-title":"French observations of disease and drug use in late 18th-century Cairo","volume":"39","author":"Estes JW","year":"1984","journal-title":"J. Hist. Med."},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1353\/jwh.2012.0044"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/35038073"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2000.1272"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-9868.2006.00553.x"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1467-9868.2009.00736.x"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v069.i12"},{"key":"e_1_3_5_43_2","first-page":"7","article-title":"Coda: convergence diagnosis and output analysis for MCMC","volume":"6","author":"Plummer M","year":"2006","journal-title":"R News"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.1214\/ss\/1177011136"},{"key":"e_1_3_5_45_2","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1080\/10618600.1998.10474787","article-title":"General methods for monitoring convergence of iterative simulations","volume":"7","author":"Brooks SPB","year":"1998","journal-title":"J. Comput. Graph. Stat."},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.3406\/remmm.1979.1845"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1728-4457.2005.00083.x"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(06)70438-8"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmm.2009.05.003"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/ae\/41.3.147"},{"key":"e_1_3_5_51_2","first-page":"733","article-title":"Posterior predictive assessment of model fitness via realized discrepancies","volume":"6","author":"Gelman A","year":"1996","journal-title":"Stat. Sin."},{"key":"e_1_3_5_52_2","first-page":"61","article-title":"The great plague of Hong Kong","volume":"15","author":"Pryor EG","year":"1975","journal-title":"J. Hong Kong Branch R. Asiat. Soc."},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1111\/1469-0691.12540"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2012.09.010"}],"container-title":["Journal of The Royal Society Interface"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rsif.2017.0160","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/full-xml\/10.1098\/rsif.2017.0160","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/royalsocietypublishing.org\/doi\/pdf\/10.1098\/rsif.2017.0160","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,24]],"date-time":"2024-06-24T18:08:55Z","timestamp":1719252535000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/doi\/10.1098\/rsif.2017.0160"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6]]},"references-count":53,"journal-issue":{"issue":"131","published-print":{"date-parts":[[2017,6]]}},"alternative-id":["10.1098\/rsif.2017.0160"],"URL":"https:\/\/doi.org\/10.1098\/rsif.2017.0160","relation":{},"ISSN":["1742-5689","1742-5662"],"issn-type":[{"value":"1742-5689","type":"print"},{"value":"1742-5662","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,6]]},"assertion":[{"value":"2017-03-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-05-30","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-06-21","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}