{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T18:18:23Z","timestamp":1780510703410,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007989","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,25]],"date-time":"2020-06-25T00:00:00Z","timestamp":1593043200000}}],"reference-count":80,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2020,6,15]],"date-time":"2020-06-15T00:00:00Z","timestamp":1592179200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R03AI135926-01A1"],"award-info":[{"award-number":["1R03AI135926-01A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["ES009089"],"award-info":[{"award-number":["ES009089"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54 GM088558"],"award-info":[{"award-number":["U54 GM088558"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the University Grants Committee of the Hong Kong Government","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}]},{"name":"the University Grants Committee of the Hong Kong Government","award":["T11-705\/14N"],"award-info":[{"award-number":["T11-705\/14N"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1007989","type":"journal-article","created":{"date-parts":[[2020,6,15]],"date-time":"2020-06-15T13:34:50Z","timestamp":1592228090000},"page":"e1007989","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":57,"title":["Dynamic interactions of influenza viruses in Hong Kong during 1998-2018"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7555-9728","authenticated-orcid":true,"given":"Wan","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6688-9637","authenticated-orcid":true,"given":"Eric H. Y.","family":"Lau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6297-7154","authenticated-orcid":true,"given":"Benjamin J.","family":"Cowling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2020,6,15]]},"reference":[{"key":"pcbi.1007989.ref001","unstructured":"World Health Organization (2016) Influenza (Seasonal), Fact Sheet. http:\/\/www.who.int\/mediacentre\/factsheets\/fs211\/en\/"},{"key":"pcbi.1007989.ref002","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1016\/S0140-6736(17)33293-2","article-title":"Estimates of global seasonal influenza-associated respiratory mortality: a modelling study","volume":"391","author":"AD Iuliano","year":"2018","journal-title":"Lancet"},{"key":"pcbi.1007989.ref003","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/nrmicro2613","article-title":"Influenza A viruses: new research developments","volume":"9","author":"RA Medina","year":"2011","journal-title":"Nature reviews Microbiology"},{"key":"pcbi.1007989.ref004","doi-asserted-by":"crossref","first-page":"e01914","DOI":"10.7554\/eLife.01914","article-title":"Integrating influenza antigenic dynamics with molecular evolution","volume":"3","author":"T Bedford","year":"2014","journal-title":"Elife"},{"key":"pcbi.1007989.ref005","doi-asserted-by":"crossref","first-page":"19359","DOI":"10.1073\/pnas.1109314108","article-title":"Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans","volume":"108","author":"J Bahl","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref006","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1126\/science.1097211","article-title":"Mapping the antigenic and genetic evolution of influenza virus","volume":"305","author":"DJ Smith","year":"2004","journal-title":"Science"},{"key":"pcbi.1007989.ref007","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1146\/annurev-med-120611-145115","article-title":"Toward a universal influenza virus vaccine: prospects and challenges","volume":"64","author":"N Pica","year":"2013","journal-title":"Annu Rev Med"},{"key":"pcbi.1007989.ref008","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1128\/JVI.02371-10","article-title":"Vaccination against seasonal influenza A\/H3N2 virus reduces the induction of heterosubtypic immunity against influenza A\/H5N1 virus infection in ferrets","volume":"85","author":"R Bodewes","year":"2011","journal-title":"J Virol"},{"key":"pcbi.1007989.ref009","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1126\/science.1171491","article-title":"Antibody recognition of a highly conserved influenza virus epitope","volume":"324","author":"DC Ekiert","year":"2009","journal-title":"Science"},{"key":"pcbi.1007989.ref010","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1126\/science.1204839","article-title":"A highly conserved neutralizing epitope on group 2 influenza A viruses","volume":"333","author":"DC Ekiert","year":"2011","journal-title":"Science"},{"key":"pcbi.1007989.ref011","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1086\/498980","article-title":"Prior H1N1 Influenza Infection and Susceptibility of Cleveland Family Study Participants during the H2N2 Pandemic of 1957: An Experiment of Nature","volume":"193","author":"SL Epstein","year":"2006","journal-title":"J Infect Dis"},{"key":"pcbi.1007989.ref012","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1056\/NEJM198307073090103","article-title":"Cytotoxic T-cell immunity to influenza","volume":"309","author":"AJ McMichael","year":"1983","journal-title":"N Engl J Med"},{"key":"pcbi.1007989.ref013","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1093\/infdis\/jis652","article-title":"1976 and 2009 H1N1 Influenza Virus Vaccines Boost Anti-Hemagglutinin Stalk Antibodies in Humans","volume":"207","author":"MS Miller","year":"2012","journal-title":"J Infect Dis"},{"key":"pcbi.1007989.ref014","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1371\/journal.pmed.0040059","article-title":"Cross-reactive neuraminidase antibodies afford partial protection against H5N1 in mice and are present in unexposed humans","volume":"4","author":"MR Sandbulte","year":"2007","journal-title":"PLoS Med"},{"key":"pcbi.1007989.ref015","first-page":"521","article-title":"Serum cross-reactive antibody response to a novel influenza A (H1N1) virus after vaccination with seasonal influenza vaccine","volume":"58","author":"J Katz","year":"2009","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"pcbi.1007989.ref016","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1126\/science.1222908","article-title":"Highly Conserved Protective Epitopes on Influenza B Viruses","volume":"337","author":"C Dreyfus","year":"2012","journal-title":"Science"},{"key":"pcbi.1007989.ref017","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1186\/1743-422X-7-351","article-title":"Conserved epitopes of influenza A virus inducing protective immunity and their prospects for universal vaccine development","volume":"7","author":"Z Stanekova","year":"2010","journal-title":"Virol J"},{"key":"pcbi.1007989.ref018","first-page":"685","article-title":"The time-interval between infections and viral hierarchies are determinants of viral interference following influenza virus infection in a ferret model","volume":"46","author":"K Laurie","year":"2016","journal-title":"Eur J Immunol"},{"key":"pcbi.1007989.ref019","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1007\/s00285-002-0186-2","article-title":"Dynamics of annual influenza A epidemics with immuno-selection","volume":"46","author":"V Andreasen","year":"2003","journal-title":"Journal of mathematical biology"},{"key":"pcbi.1007989.ref020","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.jtbi.2012.06.012","article-title":"The impact of past epidemics on future disease dynamics","volume":"309","author":"S Bansal","year":"2012","journal-title":"Journal of theoretical biology"},{"key":"pcbi.1007989.ref021","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/j.tpb.2003.10.002","article-title":"Influenza drift and epidemic size: the race between generating and escaping immunity","volume":"65","author":"MF Boni","year":"2004","journal-title":"Theor Popul Biol"},{"key":"pcbi.1007989.ref022","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.mbs.2005.12.029","article-title":"The SIRC model and influenza A","volume":"200","author":"R Casagrandi","year":"2006","journal-title":"Mathematical Biosciences"},{"key":"pcbi.1007989.ref023","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1007\/s00285-016-1000-x","article-title":"Dynamics of two-strain influenza model with cross-immunity and no quarantine class","volume":"73","author":"KW Chung","year":"2016","journal-title":"Journal of mathematical biology"},{"key":"pcbi.1007989.ref024","doi-asserted-by":"crossref","first-page":"17209","DOI":"10.1073\/pnas.252512799","article-title":"Dynamics and selection of many-strain pathogens","volume":"99","author":"JR Gog","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref025","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1007\/s002850100120","article-title":"A status-based approach to multiple strain dynamics","volume":"44","author":"JR Gog","year":"2002","journal-title":"Journal of mathematical biology"},{"key":"pcbi.1007989.ref026","doi-asserted-by":"crossref","first-page":"1898","DOI":"10.1126\/science.1132745","article-title":"Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans","volume":"314","author":"K Koelle","year":"2006","journal-title":"Science"},{"key":"pcbi.1007989.ref027","doi-asserted-by":"crossref","first-page":"e07361","DOI":"10.7554\/eLife.07361","article-title":"The effects of a deleterious mutation load on patterns of influenza A\/H3N2's antigenic evolution in humans","volume":"4","author":"K Koelle","year":"2015","journal-title":"Elife"},{"key":"pcbi.1007989.ref028","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1098\/rspb.2011.1168","article-title":"Influenza emergence in the face of evolutionary constraints","volume":"279","author":"A Kucharski","year":"2012","journal-title":"Proc R Soc B-Biol Sci"},{"key":"pcbi.1007989.ref029","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1098\/rsif.2008.0467","article-title":"Incorporating demographic stochasticity into multi-strain epidemic models: application to influenza A","volume":"6","author":"P Minayev","year":"2009","journal-title":"Journal of the Royal Society Interface"},{"key":"pcbi.1007989.ref030","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1098\/rspa.2009.0435","article-title":"Sustained oscillations in an evolutionary epidemiological model of influenza A drift","volume":"466","author":"P Magal","year":"2010","journal-title":"P R Soc A"},{"key":"pcbi.1007989.ref031","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.tpb.2006.07.002","article-title":"On the role of cross-immunity and vaccines on the survival of less fit flu-strains","volume":"71","author":"M Nuno","year":"2007","journal-title":"Theor Popul Biol"},{"key":"pcbi.1007989.ref032","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/s41598-017-01021-x","article-title":"A joint analysis of influenza-associated hospitalizations and mortality in Hong Kong, 1998\u20132013","volume":"7","author":"P Wu","year":"2017","journal-title":"Sci Rep"},{"key":"pcbi.1007989.ref033","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1016\/S2213-2600(18)30419-3","article-title":"Effectiveness of influenza vaccination on influenza-associated hospitalisations over time among children in Hong Kong: a test-negative case-control study","volume":"6","author":"S Feng","year":"2018","journal-title":"Lancet Resp Med"},{"key":"pcbi.1007989.ref034","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1109\/78.978374","article-title":"A tutorial on particle filters for online nonlinear\/non-Gaussian Bayesian tracking","volume":"50","author":"MS Arulampalam","year":"2002","journal-title":"IEEE Trans Signal Process"},{"key":"pcbi.1007989.ref035","doi-asserted-by":"crossref","first-page":"4089","DOI":"10.1175\/2009MWR2835.1","article-title":"Particle Filtering in Geophysical Systems","volume":"137","author":"PJ van Leeuwen","year":"2009","journal-title":"Mon Weather Rev"},{"key":"pcbi.1007989.ref036","doi-asserted-by":"crossref","first-page":"e1004383","DOI":"10.1371\/journal.pcbi.1004383","article-title":"Forecasting Influenza Epidemics in Hong Kong","volume":"11","author":"W Yang","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1007989.ref037","doi-asserted-by":"crossref","first-page":"e1000316","DOI":"10.1371\/journal.pbio.1000316","article-title":"Absolute humidity and the seasonal onset of influenza in the continental United States","volume":"8","author":"J Shaman","year":"2010","journal-title":"Plos Biol"},{"key":"pcbi.1007989.ref038","doi-asserted-by":"crossref","first-page":"9538","DOI":"10.1073\/pnas.1321656111","article-title":"Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers","volume":"111","author":"JB Axelsen","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref039","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1214\/11-AOS886","article-title":"Iterated filtering","volume":"39","author":"EL Ionides","year":"2011","journal-title":"Ann Stat"},{"key":"pcbi.1007989.ref040","doi-asserted-by":"crossref","first-page":"18438","DOI":"10.1073\/pnas.0603181103","article-title":"Inference for nonlinear dynamical systems","volume":"103","author":"EL Ionides","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref041","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1073\/pnas.1410597112","article-title":"Inference for dynamic and latent variable models via iterated, perturbed Bayes maps","volume":"112","author":"EL Ionides","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref042","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.1007989.ref043","article-title":"A simple modification for improving inference of non-linear dynamical systems","author":"W Yang","year":"2014","journal-title":"arXiv"},{"key":"pcbi.1007989.ref044","doi-asserted-by":"crossref","first-page":"538","DOI":"10.3201\/eid1603.091216","article-title":"School closure and mitigation of pandemic (H1N1) 2009, Hong Kong","volume":"16","author":"JT Wu","year":"2010","journal-title":"Emerging infectious diseases"},{"key":"pcbi.1007989.ref045","doi-asserted-by":"crossref","first-page":"e13350","DOI":"10.1371\/journal.pone.0013350","article-title":"Situational awareness and health protective responses to pandemic influenza A (H1N1) in Hong Kong: a cross-sectional study","volume":"5","author":"Q Liao","year":"2010","journal-title":"Plos One"},{"key":"pcbi.1007989.ref046","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1111\/j.1750-2659.2011.00234.x","article-title":"Transmission parameters of the A\/H1N1 (2009) influenza virus pandemic: a review","volume":"5","author":"PY Boelle","year":"2011","journal-title":"Influenza Other Respir Viruses"},{"key":"pcbi.1007989.ref047","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1038\/s41467-019-09652-6","article-title":"Age-specific differences in the dynamics of protective immunity to influenza","volume":"10","author":"S Ranjeva","year":"2019","journal-title":"Nat Commun"},{"key":"pcbi.1007989.ref048","doi-asserted-by":"crossref","first-page":"e1002082","DOI":"10.1371\/journal.pbio.1002082","article-title":"Estimating the life course of influenza A(H3N2) antibody responses from cross-sectional data","volume":"13","author":"AJ Kucharski","year":"2015","journal-title":"Plos Biol"},{"key":"pcbi.1007989.ref049","doi-asserted-by":"crossref","first-page":"e1001051","DOI":"10.1371\/journal.pmed.1001051","article-title":"Predicting the epidemic sizes of influenza A\/H1N1, A\/H3N2, and B: a statistical method","volume":"8","author":"E Goldstein","year":"2011","journal-title":"PLoS Med"},{"key":"pcbi.1007989.ref050","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1126\/science.1097211","article-title":"Mapping the antigenic and genetic evolution of influenza virus","volume":"305","author":"DJ Smith","year":"2004","journal-title":"Science"},{"key":"pcbi.1007989.ref051","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1186\/1471-2334-14-480","article-title":"Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature","volume":"14","author":"M Biggerstaff","year":"2014","journal-title":"Bmc Infect Dis"},{"key":"pcbi.1007989.ref052","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1093\/aje\/kwm375","article-title":"Time lines of infection and disease in human influenza: a review of volunteer challenge studies","volume":"167","author":"F Carrat","year":"2008","journal-title":"Am J Epidemiol"},{"key":"pcbi.1007989.ref053","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1093\/cid\/ciu356","article-title":"Incidence of influenza virus infections in children in Hong Kong in a 3-year randomized placebo-controlled vaccine study, 2009\u20132012","volume":"59","author":"BJ Cowling","year":"2014","journal-title":"Clinical infectious diseases: an official publication of the Infectious Diseases Society of America"},{"key":"pcbi.1007989.ref054","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1093\/infdis\/jiz201","article-title":"Birth Cohort Effects in Influenza Surveillance Data: Evidence That First Influenza Infection Affects Later Influenza-Associated Illness","volume":"220","author":"AP Budd","year":"2019","journal-title":"The Journal of infectious diseases"},{"key":"pcbi.1007989.ref055","unstructured":"NextStrain.org (2019) Real-time tracking of influenza A\/H1N1pdm evolution. https:\/\/nextstrain.org\/flu\/seasonal\/h1n1pdm\/ha\/12y?c=cTiter&f_country=hong_kong"},{"key":"pcbi.1007989.ref056","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1093\/cid\/cix1060","article-title":"Seasonal Incidence of Symptomatic Influenza in the United States","volume":"66","author":"JI Tokars","year":"2018","journal-title":"Clinical Infectious Diseases"},{"key":"pcbi.1007989.ref057","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/infdis\/jiy443","article-title":"Risk Factors and Attack Rates of Seasonal Influenza Infection: Results of the Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance (SHIVERS) Seroepidemiologic Cohort Study","volume":"219","author":"QS Huang","year":"2019","journal-title":"Journal of Infectious Diseases"},{"key":"pcbi.1007989.ref058","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.4161\/hv.25490","article-title":"Concerns for low coverage of influenza vaccination in middle-aged adults","volume":"9","author":"SS Lee","year":"2013","journal-title":"Human vaccines & immunotherapeutics"},{"key":"pcbi.1007989.ref059","unstructured":"Centre for Health, Protection Department of Health, The Govenment of the Hong Kong Special Administrative Region (2017) Statistics on 2016\/17 Vaccination Programmes\/Schemes http:\/\/www.chp.gov.hk\/en\/view_content\/26734.html"},{"key":"pcbi.1007989.ref060","unstructured":"Centers for Disease Control and Prevention (2016) National Early-Season Flu Vaccination Coverage, United States, November 2016. https:\/\/www.cdc.gov\/flu\/fluvaxview\/nifs-estimates-nov2016.htm"},{"key":"pcbi.1007989.ref061","doi-asserted-by":"crossref","first-page":"e1004054","DOI":"10.1371\/journal.ppat.1004054","article-title":"Inferring influenza infection attack rate from seroprevalence data","volume":"10","author":"JT Wu","year":"2014","journal-title":"PLoS Pathog"},{"key":"pcbi.1007989.ref062","doi-asserted-by":"crossref","first-page":"e38346","DOI":"10.1371\/journal.pone.0038346","article-title":"Situational Awareness of Influenza Activity Based on Multiple Streams of Surveillance Data Using Multivariate Dynamic Linear Model","volume":"7","author":"EHY Lau","year":"2012","journal-title":"Plos One"},{"key":"pcbi.1007989.ref063","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.3201\/eid1407.080060","article-title":"Optimizing use of multistream influenza sentinel surveillance data","volume":"14","author":"EHY Lau","year":"2008","journal-title":"Emerging infectious diseases"},{"key":"pcbi.1007989.ref064","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1093\/ije\/dyl162","article-title":"Methods for monitoring influenza surveillance data","volume":"35","author":"BJ Cowling","year":"2006","journal-title":"International journal of epidemiology"},{"key":"pcbi.1007989.ref065","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.1007989.ref066","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1093\/aje\/kws314","article-title":"Infection fatality risk of the pandemic A(H1N1)2009 virus in Hong Kong","volume":"177","author":"JY Wong","year":"2013","journal-title":"Am J Epidemiol"},{"key":"pcbi.1007989.ref067","doi-asserted-by":"crossref","first-page":"2723","DOI":"10.1073\/pnas.1415012112","article-title":"Inference of seasonal and pandemic influenza transmission dynamics","volume":"112","author":"W Yang","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1007989.ref068","doi-asserted-by":"crossref","first-page":"e1000442","DOI":"10.1371\/journal.pmed.1000442","article-title":"Epidemiological characteristics of 2009 (H1N1) pandemic influenza based on paired sera from a longitudinal community cohort study","volume":"8","author":"S Riley","year":"2011","journal-title":"PLoS Med"},{"key":"pcbi.1007989.ref069","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1097\/EDE.0000000000000408","article-title":"Interpreting Seroepidemiologic Studies of Influenza in a Context of Nonbracketing Sera","volume":"27","author":"TK Tsang","year":"2016","journal-title":"Epidemiology (Cambridge, Mass)"},{"key":"pcbi.1007989.ref070","doi-asserted-by":"crossref","first-page":"13396","DOI":"10.1073\/pnas.1516698112","article-title":"Cross-immunity between strains explains the dynamical pattern of paramyxoviruses","volume":"112","author":"S Bhattacharyya","year":"2015","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007989.ref071","doi-asserted-by":"crossref","first-page":"C15","DOI":"10.1016\/j.vaccine.2008.04.008","article-title":"The impact of evolutionary constraints on influenza dynamics","volume":"26","author":"JR Gog","year":"2008","journal-title":"Vaccine"},{"key":"pcbi.1007989.ref072","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1137\/S003613990343882X","article-title":"Dynamics of Two-Strain Influenza with Isolation and Partial Cross-Immunity","volume":"65","author":"M Nu\u00f1o","year":"2005","journal-title":"SIAM Journal on Applied Mathematics"},{"key":"pcbi.1007989.ref073","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1098\/rsif.2010.0007","article-title":"A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza","volume":"7","author":"K Koelle","year":"2010","journal-title":"Journal of the Royal Society Interface"},{"key":"pcbi.1007989.ref074","doi-asserted-by":"crossref","first-page":"3173","DOI":"10.1073\/pnas.1113342109","article-title":"Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza","volume":"109","author":"N Arinaminpathy","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007989.ref075","unstructured":"Inoue E, King A Iterated filtering: principles and practice. https:\/\/kingaa.github.io\/sbied\/mif\/mif.html"},{"key":"pcbi.1007989.ref076","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1038\/nature01509","article-title":"Ecological and immunological determinants of influenza evolution","volume":"422","author":"NM Ferguson","year":"2003","journal-title":"Nature"},{"key":"pcbi.1007989.ref077","doi-asserted-by":"crossref","first-page":"20130298","DOI":"10.1098\/rsif.2013.0298","article-title":"Modelling seasonal influenza: the role of weather and punctuated antigenic drift","volume":"10","author":"R Yaari","year":"2013","journal-title":"J R Soc Interface"},{"key":"pcbi.1007989.ref078","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1186\/1471-2288-9-57","article-title":"Combining estimates of interest in prognostic modelling studies after multiple imputation: current practice and guidelines","volume":"9","author":"A Marshall","year":"2009","journal-title":"BMC Med Res Methodol"},{"key":"pcbi.1007989.ref079","volume-title":"Multiple imputation for nonresponse in surveys","author":"DB Rubin","year":"2004"},{"key":"pcbi.1007989.ref080","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v070.i08","article-title":"flexsurv: a platform for parametric survival modeling in R","volume":"70","author":"CH Jackson","year":"2016","journal-title":"Journal of Statistical Software"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007989","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,6,25]],"date-time":"2020-06-25T00:00:00Z","timestamp":1593043200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007989","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,25]],"date-time":"2020-06-25T14:15:56Z","timestamp":1593094556000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007989"}},"subtitle":[],"editor":[{"given":"Cecile","family":"Viboud","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,6,15]]},"references-count":80,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2020,6,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007989","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/19008987","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,15]]}}}