{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T19:14:23Z","timestamp":1775243663125,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010218","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,7,8]],"date-time":"2022-07-08T00:00:00Z","timestamp":1657238400000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["NO. 81703323"],"award-info":[{"award-number":["NO. 81703323"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["NO. 81773497"],"award-info":[{"award-number":["NO. 81773497"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Key Research and Development Program of China","award":["2018YFA0606200"],"award-info":[{"award-number":["2018YFA0606200"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>As a common vector-borne disease, dengue fever remains challenging to predict due to large variations in epidemic size across seasons driven by a number of factors including population susceptibility, mosquito density, meteorological conditions, geographical factors, and human mobility. An ensemble forecast system for dengue fever is first proposed that addresses the difficulty of predicting outbreaks with drastically different scales. The ensemble forecast system based on a susceptible-infected-recovered (SIR) type of compartmental model coupled with a data assimilation method called the ensemble adjusted Kalman filter (EAKF) is constructed to generate real-time forecasts of dengue fever spread dynamics. The model was informed by meteorological and mosquito density information to depict the transmission of dengue virus among human and mosquito populations, and generate predictions. To account for the dramatic variations of outbreak size in different seasons, the effective population size parameter that is sequentially updated to adjust the predicted outbreak scale is introduced into the model. Before optimizing the transmission model, we update the effective population size using the most recent observations and historical records so that the predicted outbreak size is dynamically adjusted. In the retrospective forecast of dengue outbreaks in Guangzhou, China during the 2011\u20132017 seasons, the proposed forecast model generates accurate projections of peak timing, peak intensity, and total incidence, outperforming a generalized additive model approach. The ensemble forecast system can be operated in real-time and inform control planning to reduce the burden of dengue fever.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010218","type":"journal-article","created":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T17:35:33Z","timestamp":1656351333000},"page":"e1010218","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China"],"prefix":"10.1371","volume":"18","author":[{"given":"Yuliang","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1451-5251","authenticated-orcid":true,"given":"Tao","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9248-9568","authenticated-orcid":true,"given":"Xiaolin","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qinghui","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zixi","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haisheng","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qingying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianpeng","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenjun","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7072-2995","authenticated-orcid":true,"given":"Sen","family":"Pei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0990-6461","authenticated-orcid":true,"given":"Pi","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,6,27]]},"reference":[{"key":"pcbi.1010218.ref001","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/0-387-33026-7_3","volume-title":"Hot Topics in Infection and Immunity in Children III","author":"P Hotez","year":"2006"},{"key":"pcbi.1010218.ref002","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nature12060","article-title":"The global distribution and burden of dengue","volume":"496","author":"S Bhatt","year":"2013","journal-title":"Nature"},{"key":"pcbi.1010218.ref003","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1038\/nrmicro2460","article-title":"Dengue: a continuing global threat","volume":"8","author":"MG Guzman","year":"2010","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1010218.ref004","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.jtbi.2016.04.008","article-title":"Modelling the effect of temperature on the seasonal population dynamics of temperate mosquitoes","volume":"400","author":"DA Ewing","year":"2016","journal-title":"J Theor Biol"},{"key":"pcbi.1010218.ref005","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1186\/s13071-018-3045-8","article-title":"Mosquitoes (Diptera: Culicidae) and mosquito-borne diseases in Mali, West Africa","volume":"11","author":"F Tandina","year":"2018","journal-title":"Parasit Vectors"},{"key":"pcbi.1010218.ref006","unstructured":"The Data-center of China Public Health Science. Available: http:\/\/www.phsciencedata.cn"},{"key":"pcbi.1010218.ref007","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1111\/j.0006-341X.2000.01030.x","article-title":"Zero-inflated Poisson and binomial regression with random effects: a case study","volume":"56","author":"DB Hall","year":"2000","journal-title":"Biometrics"},{"key":"pcbi.1010218.ref008","doi-asserted-by":"crossref","first-page":"24268","DOI":"10.1073\/pnas.1909865116","article-title":"An open challenge to advance probabilistic forecasting for dengue epidemics","volume":"116","author":"MA Johansson","year":"2019","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010218.ref009","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1093\/aje\/kwg239","article-title":"Prediction of the spread of influenza epidemics by the method of analogues","volume":"158","author":"C Viboud","year":"2003","journal-title":"Am J Epidemiol"},{"key":"pcbi.1010218.ref010","doi-asserted-by":"crossref","first-page":"e1004382","DOI":"10.1371\/journal.pcbi.1004382","article-title":"Flexible Modeling of Epidemics with an Empirical Bayes Framework","volume":"11","author":"LC Brooks","year":"2015","journal-title":"PLoS Comput Biol."},{"key":"pcbi.1010218.ref011","doi-asserted-by":"crossref","first-page":"e3063","DOI":"10.1371\/journal.pntd.0003063","article-title":"Risk of dengue for tourists and teams during the World Cup 2014 in Brazil","volume":"8","author":"WG van Panhuis","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"key":"pcbi.1010218.ref012","doi-asserted-by":"crossref","first-page":"e0195065","DOI":"10.1371\/journal.pone.0195065","article-title":"Dengue forecasting in S\u00e3o Paulo city with generalized additive models, artificial neural networks and seasonal autoregressive integrated moving average models","volume":"13","author":"OS Baquero","year":"2018","journal-title":"PLoS One"},{"key":"pcbi.1010218.ref013","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1038\/s41467-017-01033-1","article-title":"Counteracting structural errors in ensemble forecast of influenza outbreaks","volume":"8","author":"S Pei","year":"2017","journal-title":"Nat Commun"},{"key":"pcbi.1010218.ref014","doi-asserted-by":"crossref","first-page":"e1000471","DOI":"10.1371\/journal.pcbi.1000471","article-title":"Temporal variability and social heterogeneity in disease transmission: the case of SARS in Hong Kong","volume":"5","author":"A Cori","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010218.ref015","doi-asserted-by":"crossref","first-page":"20160410","DOI":"10.1098\/rsif.2016.0410","article-title":"Superensemble forecasts of dengue outbreaks","volume":"13","author":"TK Yamana","year":"2016","journal-title":"J R Soc Interface"},{"key":"pcbi.1010218.ref016","doi-asserted-by":"crossref","first-page":"14592","DOI":"10.1038\/ncomms14592","article-title":"Ensemble forecast of human West Nile virus cases and mosquito infection rates","volume":"8","author":"NB DeFelice","year":"2017","journal-title":"Nat Commun"},{"key":"pcbi.1010218.ref017","doi-asserted-by":"crossref","first-page":"4895","DOI":"10.1038\/s41598-018-23075-1","article-title":"Prediction of influenza-like illness based on the improved artificial tree algorithm and artificial neural network","volume":"8","author":"H Hu","year":"2018","journal-title":"Sci Rep."},{"key":"pcbi.1010218.ref018","doi-asserted-by":"crossref","first-page":"20200691","DOI":"10.1098\/rsif.2020.0691","article-title":"Predicting dengue outbreaks at neighbourhood level using human mobility in urban areas","volume":"17","author":"R Bomfim","year":"2020","journal-title":"J R Soc Interface"},{"key":"pcbi.1010218.ref019","doi-asserted-by":"crossref","first-page":"20425","DOI":"10.1073\/pnas.1208772109","article-title":"Forecasting seasonal outbreaks of influenza","volume":"109","author":"J Shaman","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010218.ref020","doi-asserted-by":"crossref","first-page":"2752","DOI":"10.1073\/pnas.1708856115","article-title":"Forecasting the spatial transmission of influenza in the United States","volume":"115","author":"S Pei","year":"2018","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010218.ref021","first-page":"6","article-title":"Inference and forecast of the current west african ebola outbreak in Guinea, sierra leone and liberia","author":"J Shaman","year":"2014","journal-title":"PLoS Curr"},{"key":"pcbi.1010218.ref022","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/s41467-020-20399-3","article-title":"Optimizing respiratory virus surveillance networks using uncertainty propagation","volume":"12","author":"S Pei","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1010218.ref023","doi-asserted-by":"crossref","first-page":"2884","DOI":"10.1175\/1520-0493(2001)129<2884:AEAKFF>2.0.CO;2","article-title":"An Ensemble Adjustment Kalman Filter for Data Assimilation","volume":"129","author":"JL Anderson","year":"2001","journal-title":"Mon Wea Rev."},{"key":"pcbi.1010218.ref024","volume-title":"Dengue and dengue hemorrhagic fever","author":"C.A.B. International","edition":"2"},{"key":"pcbi.1010218.ref025","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1475-925X-2-4","article-title":"A model of dengue fever.","volume":"2","author":"M Derouich","year":"2003","journal-title":"BioMed Eng OnLine"},{"key":"pcbi.1010218.ref026","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1093\/jmedent\/29.6.985","article-title":"Variation in the efficiency of vertical transmission of dengue-1 virus by strains of Aedes albopictus (Diptera: Culicidae)","volume":"29","author":"CF Bosio","year":"1992","journal-title":"J Med Entomol"},{"key":"pcbi.1010218.ref027","doi-asserted-by":"crossref","first-page":"2337","DOI":"10.3389\/fmicb.2017.02337","article-title":"Temperature Increase Enhances Aedes albopictus Competence to Transmit Dengue Virus","volume":"8","author":"Z Liu","year":"2017","journal-title":"Front Microbiol."},{"key":"pcbi.1010218.ref028","doi-asserted-by":"crossref","first-page":"100344","DOI":"10.1016\/j.epidem.2019.05.003","article-title":"Temperature impacts on dengue emergence in the United States: Investigating the role of seasonality and climate change","volume":"28","author":"MA Robert","year":"2019","journal-title":"Epidemics"},{"key":"pcbi.1010218.ref029","doi-asserted-by":"crossref","first-page":"e0229829","DOI":"10.1371\/journal.pone.0229829","article-title":"Semi-field life-table studies of Aedes albopictus (Diptera: Culicidae) in Guangzhou, China","volume":"15","author":"D Yang","year":"2020","journal-title":"PLoS One"},{"key":"pcbi.1010218.ref030","doi-asserted-by":"crossref","first-page":"e0226841","DOI":"10.1371\/journal.pone.0226841","article-title":"A dengue fever predicting model based on Baidu search index data and climate data in South China","volume":"14","author":"D Liu","year":"2019","journal-title":"PLoS One"},{"key":"pcbi.1010218.ref031","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1073\/pnas.1618558114","article-title":"Climate variation drives dengue dynamics","volume":"114","author":"L Xu","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010218.ref032","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.1590\/S0102-311X2011000900014","article-title":"Predicting the number of cases of dengue infection in Ribeir\u00e3o Preto, S\u00e3o Paulo State, Brazil, using a SARIMA model","volume":"27","author":"EZ Martinez","year":"2011","journal-title":"Cad Saude Publica"},{"key":"pcbi.1010218.ref033","first-page":"08","article-title":"A Survey of Mathematical Models of Dengue Fever","author":"IB James Braselton","year":"2015","journal-title":"J Comput Sci Syst Biol"},{"key":"pcbi.1010218.ref034","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1111\/tmi.13147","article-title":"Burden of dengue among febrile patients at the time of chikungunya introduction in Piedecuesta, Colombia","volume":"23","author":"M Carabali","year":"2018","journal-title":"Trop Med Int Health"},{"key":"pcbi.1010218.ref035","doi-asserted-by":"crossref","first-page":"e0006650","DOI":"10.1371\/journal.pntd.0006650","article-title":"Estimating dengue under-reporting in Puerto Rico using a multiplier model","volume":"12","author":"MB Shankar","year":"2018","journal-title":"PLoS Negl Trop Dis"},{"key":"pcbi.1010218.ref036","doi-asserted-by":"crossref","first-page":"e102755","DOI":"10.1371\/journal.pone.0102755","article-title":"Predicting local dengue transmission in Guangzhou, China, through the influence of imported cases, mosquito density and climate variability","volume":"9","author":"S Sang","year":"2014","journal-title":"PLoS One"},{"key":"pcbi.1010218.ref037","doi-asserted-by":"crossref","first-page":"321","DOI":"10.3201\/eid1702.100396","article-title":"Dengue virus serotype 3 subtype III, Zhejiang Province, China","volume":"17","author":"J Sun","year":"2011","journal-title":"Emerg Infect Dis"},{"key":"pcbi.1010218.ref038","first-page":"26","article-title":"The design and efficacy observation of new mosq\u2014ovitrap for monitoring of vector of dengue fever","volume":"16","author":"L Lin","year":"2005","journal-title":"Chinese Journal of Vector Biology and Control"},{"key":"pcbi.1010218.ref039","doi-asserted-by":"crossref","first-page":"2837","DOI":"10.1038\/ncomms3837","article-title":"Real-time influenza forecasts during the 2012\u20132013 season","volume":"4","author":"J Shaman","year":"2013","journal-title":"Nat Commun"},{"key":"pcbi.1010218.ref040","doi-asserted-by":"crossref","first-page":"e1003583","DOI":"10.1371\/journal.pcbi.1003583","article-title":"Comparison of filtering methods for the modeling and retrospective forecasting of influenza epidemics","volume":"10","author":"W Yang","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1010218.ref041","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1038\/s41467-019-09035-x","article-title":"Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China","volume":"10","author":"RJ Oidtman","year":"2019","journal-title":"Nat Commun"},{"key":"pcbi.1010218.ref042","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.mbs.2017.04.005","article-title":"An SIR-Dengue transmission model with seasonal effects and impulsive control","volume":"289","author":"J P\u00e1ez Ch\u00e1vez","year":"2017","journal-title":"Math Biosci"},{"key":"pcbi.1010218.ref043","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1186\/1756-3305-7-338","article-title":"Global temperature constraints on Aedes aegypti and Ae. albopictus persistence and competence for dengue virus transmission","volume":"7","author":"OJ Brady","year":"2014","journal-title":"Parasit Vectors"},{"key":"pcbi.1010218.ref044","first-page":"44","article-title":"Geographic spread of Aedes albopictus and potential for involvement in arbovirus cycles in the Mediterranean basin","volume":"20","author":"CJ Mitchell","year":"1995","journal-title":"Journal of Vector Ecology"},{"key":"pcbi.1010218.ref045","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7601\/mez.58.1_1","article-title":"Seasonal changes in oviposition activity, hatching and embryonation rates of eggs of Aedes albopictus (Diptera: Culicidae) on three islands of the Ryukyu Archipelago, Japan","volume":"58","author":"Y Higa","year":"2007","journal-title":"Med Entomol Zool"},{"key":"pcbi.1010218.ref046","doi-asserted-by":"crossref","first-page":"11802","DOI":"10.1073\/pnas.0602960103","article-title":"Ecological and immunological determinants of dengue epidemics","volume":"103","author":"HJ Wearing","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1010218.ref047","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1038\/s41598-018-19168-6","article-title":"Spatial and Temporal Characteristics of 2014 Dengue Outbreak in Guangdong, China","volume":"8","author":"M Sanna","year":"2018","journal-title":"Sci Rep."},{"key":"pcbi.1010218.ref048","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/imammb\/dqt002","article-title":"A model for the spatial transmission of dengue with daily movement between villages and a city","volume":"31","author":"AL Nevai","year":"2014","journal-title":"Math Med Biol"},{"key":"pcbi.1010218.ref049","doi-asserted-by":"crossref","first-page":"149","DOI":"10.15585\/mmwr.mm6906a1","article-title":"Travel-Associated and Locally Acquired Dengue Cases\u2014United States, 2010\u20132017","volume":"69","author":"A Rivera","year":"2020","journal-title":"MMWR Morb Mortal Wkly Rep."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010218","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,7,8]],"date-time":"2022-07-08T00:00:00Z","timestamp":1657238400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010218","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,8]],"date-time":"2022-07-08T18:20:12Z","timestamp":1657304412000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010218"}},"subtitle":[],"editor":[{"given":"Benjamin","family":"Althouse","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,6,27]]},"references-count":49,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010218","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1010218","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,27]]}}}