Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

Oral Program

Tuesday 28th November 2017 11:00-13:00 Pre Conference Workshop Registration I Tramuntana foyer 13:00-17:30 Pre Conference Workshop (Registration required) I Tramuntana 1 17:00-19:00 Registration I Tramuntana foyer 19:00-20:30 Welcome Reception & Poster Session 1 I Tramuntana I Wednesday 29th November 2017 07:30-08:30 Registration I Tramuntana foyer Room Tramuntana II/III 08:30-08:40 Welcome & Opening Remarks by Conference Chairs 08:40-09:10 [PLN01] Roy Anderson, Imperial College London, UK

09:10-09:50 [PLN02] Liz Corbett, London School of Hygiene and Tropical Medicine, UK

09:50-10:30 [PLN03] Caroline Buckee, Harvard School of Public Health, USA

10:30-11:10 [PLN04] Marc Bonten, University Medical Center Utrecht, The Netherlands

11:10-11:40 Refreshment Break I Hall Tramuntana Rooms Tramuntana II/III Mestral Garbi 11:40-13:00 Session 1: AMR 1 Session 2: Contact Session 3: Evolution Session Chair: TBC Session Chair: TBC Session Chair: TBC 11:40-12:00 [O1.1] Why sensitive bacteria are [O2.1] Impact of regular school [O3.1] Diversity of multiple resistant to hospital closure on seasonal influenza infection patterns and virulence control epidemics evolution E. van Kleef*1 ,2, N. Luangasanatip3, G. De Luca1, K. Van Kerckhove2, P. M.T. Sofonea*, S. Alizon, M.J.M. Bonten1, B.S. Cooper1 Coletti2, C. Poletto1, N. Bossuyt3, N. Y. Michalakis, MIVEGEC, France ,4, 1University Medical Center Hens2 ,4, V. Colizza*1 ,5, 1Inserm, Utrecht, The Netherlands, France, 2Hasselt University, Belgium, 2Mahidol-Oxford Tropical Medicine 3Scientific Institute of Public Health, Research Unit, Thailand, 3London Belgium, 4University of Antwerp, School of Hygiene and Tropical Belgium, 5ISI Foundation, Italy Medicine, UK, 4University of Oxford, UK 12:00-12:20 [O1.2] Ecological association [O2.2] Quantifying the [O3.2] Neutral mutations and between unequal antibiotic effectiveness of contact tracing selection drive pervasive loss of consumption and antibiotic efforts using mathmatical mutability in long-lived B cell resistance modeling: The 2014 Ebola outbreak lineages during chronic HIV S.W. Olesen*1, M.L. Barnett1 ,2, D. in Mali as a case study infection MacFadden1 ,3, M. Lipsitch1, Y.H. L.F. Moriarty*, G. Chowell, Georgia M. Vieira*, D. Zinder, S. Grad1 ,2, 1Harvard T. H. Chan State University, USA Cobey, University of Chicago, School of Public Health, USA, USA 2Brigham and Women's Hospital, USA, 3University of Toronto, 12:20-12:40 [O1.3] Elucidating plausible [O2.3] A nonparametric method for [O3.3] Real-time genomic mechanisms of coexistence helps simulating sexual contact networks surveillance of pathogen predict the impact of vaccination using limited data: applications to evolution and spread upon antibiotic resistance the South African HIV epidemic T. Bedford, Fred Hutchinson N.G. Davies*, S. Flasche, M. Jit, K.E. K.A. Risher*1 ,2, D.D. Celentano2, S.H. Cancer Research Center, USA Atkins, London School of Hygiene Mehta2, L. Simbayi3, O. Shisana4, T. & Tropical Medicine, UK Rehle3 ,5, J. Lessler2, 1London School of Hygiene and Tropical Medicine, UK, 2Johns Hopkins Bloomberg School of Public Health, USA, Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

3Human Sciences Research Council, South Africa, 4Evidence Based Solutions, South Africa, 5University of Cape Town, South Africa 12:40-13:00 [O1.4] An evolutionary model to [O2.4] Participatory development [O3.4] Detecting signatures of predict the frequency of antibiotic of a contact diary tool to capture transmission reduction on the resistance under seasonal dynamic household structure and road to eradication antibiotic use, and an application mobility within and between G. Rydevik, S. Lycett*, University to Streptococcus pneumoniae remote Aboriginal and Torres Strait of Edinburgh, UK F. Blanquart*, S. Lehtinen, C. Islander communities Fraser, , UK J. McVernon*1 ,2, K. Gibney1, S. Hanieh1, B. Biggs1, J. Shield1, B. Davison3, G. Singh3 ,4, T. Kearns3, M. McKinnon3, R.G. Dhurrkay3, 1The Royal Melbourne Hospital and the University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Australia, 2The University of Melbourne, Australia, 3Menzies School of Health Research, Australia, 4Northern Territory Medical Program of Flinders and James Cook Universities, Australia, 5Miwatj Health Aboriginal Corporation, Australia, 6University of Melbourne, Australia, 7University of Melbourne, Australia 13:00-14:00 Lunch | Noray Restaurant 13:00-14:00 Author Workshop I TBC Rooms Tramuntana II/III Mestral Garbi 14:00-15:40 Session 4: Influenza 1 Session 5: Genetic diversity Session 6: Social & network Session Chair: TBC Session Chair: TBC Session Chair: TBC 14:00-14:20 [O4.1] Collaborative efforts to [O5.1] Phyloscanner: Analysing [O6.1] A data-driven social routinely forecast seasonal within- and between-host behavioural model influenza in the United States pathogen genetic diversity to for individual vaccination across four influenza seasons, identify transmission, multiple decisions 2013-14 to 2016-17 infection, recombination and J.J. Hoogink*1 ,2, D.W.F. van M. Biggerstaff*, C. McGowan, M. contamination Krevelen1, J. Wallinga1 Johansson, C. Reed, Centers for C. Wymant*1 ,2, M. Hall1 ,2, O. ,2, 1National Institute for Public Disease Control and Prevention, Ratmann2, D. Bonsall1, T. Health and Environment, The USA Golubchik1, M. de Cesare1, A. Gall3, Netherlands, 2Leiden University M. Cornelissen4, C. Fraser1 Medical Center, The Netherlands ,2, 1University of Oxford, UK, 2Imperial College London, UK, 3University of Cambridge, UK, 4University of Amsterdam, The Netherlands [O5.2] Resolving HIV-1 transmission between agrarian, trading and fisherfolk communities in Rakai, Uganda, with deep sequencing data O. Ratmann*1, M.K. Grabowski2 ,3, M. Hall4, T. Golubchik4, C. Wymant4, T. Quinn5 ,3, M. Wawer2 ,3, D. Serwadda3 ,6, R. Gray2 ,3, C. Fraser4, 1Imperial College London, UK, 2Johns Hopkins Bloomberg School of Public Health, USA, 3Rakai Health Sciences Program, Uganda, 4University of Oxford, UK, 5National Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

Institute of Allergy and Infectious Diseases, USA, 6Makerere University School of Public Health, Uganda 14:20-14:40 [O4.2] Forecasting the spatial [O5.3] Using phyloscanner to [O6.2] Statistical estimation of transmission of influenza in the identify HIV transmission clusters network models from United States and epidemiological correlates of egocentrically sampled network S. Pei*, S. Kandula, W. Yang, J. transmission data M. Morris*1, P.N. Shaman, Columbia University, USA M.D. Hall*1, C. Wymant1, O. Krivitsky2, 1University of Ratmann2, C. Fraser1, 1University of Washington, USA, 2University of Oxford, UK, 2Imperial College Wollongong, Australia London, UK 14:40-15:00 [O4.3] Predicting influenza - how [O5.4] Large variations in HIV-1 [O6.3] Nipah virus human forecast accuracy improves with viral load explained by shifting- transmission chains: Risk factors earlier data availability mosaic metapopulation dynamics and opportunities for control C. Zimmer*, S. Leuba, R. Yaesoubi, K.A. Lythgoe1 ,2, F. Blanquart1 ,2, L. B. Nikolay*1, H. Salje1, M.J. T. Cohen, Yale University, USA Pellis*3, C. Fraser1 ,2, 1University of Hossain2 ,3, A.K.M.D. Khan1, Oxford, UK, 2Imperial College H.M.S. Sazzad1, J. Pulliam1, A. M. London, UK, 3University of Warwick, Kilpatrick1, S. Sultana1, S. Afroj1, UK S.P. Luby1, E.S. Gurley1, S. Cauchemez1, 1Institut Pasteur, France, 2Medical Research Council Unit, Gambia, 3icddr,b, Bangladesh 15:00-15:20 [O4.4] Immune history and [O5.5] The Virome of Manhattan: A [O6.4] Spread of hospital- forecasting the evolution of testbed for radically advancing acquired : A seasonal influenza virus understanding and forecast of viral comparison of healthcare K. Kim*1, S. Hensley2, S. respiratory infections networks Cobey1, 1The University of Chicago, J. Shaman*1 ,2, P. Planet2 ,3, R. N. Nekkab*1 ,2, P. Astagneau3 ,4, L. USA, 2The University of Rabadan1, W. Chung1, S. Anthony1, Temime1 ,2, P. Crépey3 Pennsylvania, USA D. Hsu1, G. Freyer1, 1Columbia ,6, 1Conservatoire National des University, USA, 2American Museum Arts et Métiers, France, 2Institut of Natural History, USA, 3University Pasteur, France, 3Ecole des of Pennsylvania, USA Hautes Etudes en Santé Publique, France, 4Centre de prévention des infections associées aux soins, France, 5Sorbonne Universités, France, 6Faculté de Médecine- Timone, France, 7Université de Rennes 1, France 15:20-15:40 [O4.5] Comparison of ensemble [O5.6] What drives antigenic [O6.5] A novel methodology to methods for forecasting influenza diversity in pathogenic bacteria? study the uncertainty in the in the United States Insights from integrated genomic structure of contact leading to N.G. Reich*, A. Tushar, G.C. approaches transmission Gibson, E.L. Ray, University of R.J. Mostowy, Imperial College M. Baguelin*1 ,2, E. van Leeuwen1 Massachusetts Amerst, USA London, UK ,3, P. Klepac1 ,3, N. Demiris4, 1Public Health England, UK, 2London School of Hygiene and Tropical Medicine, UK, 3Imperial College London, UK, 4Athens University of Economics and Business, Greece

Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

15:40-16:10 Refreshment Break I Hall Tramuntana Rooms Tramuntana II/III Mestral Garbi 16:10-17:50 Session 7: Phylodynamics 1 Session 8: Dengue Session 9: Vaccination 1 Session Chair: TBC Session Chair: TBC Session Chair: TBC 16:10-16:30 [O7.1] Estimating household [O8.1] Identifying novel zoonotic [O9.1] Multiple infections: mosquito biting propensities and viruses from hospital patients with Taming combinatorial identifying hotspots for diseases of unknown origin using complexity provides insights intervention metagenomics and multivariate into HPV S.Y. Kang*1, D. Bisanzio1, D.L. statistical techniques S. Alizon*1 ,2, C.L. Murall1 ,3, E. Smith2, 1University of oxford, UK, G.S. Robertson*, J.L. Ashworth, L. Saulnier3 ,1, M. Sofonea3 2University of Washington, UK Lu, M.E.J. Woolhouse, University of ,1, 1CNRS, France, 2IRD, France, Edinburgh, UK 3Université de Montpellier, France 16:30-16:50 [O7.2] Understanding the decline [O8.2] Real-time West Nile virus [O9.2] Prior illness provides and rebound in immunity to forecasts for the 2017 season short-term protection against symptomatic malaria due to N. DeFelice*, J. Shaman, Columbia respiratory illness, but is a risk intervention disruption in malaria University, USA factor for gastroenteritis: transmission Pathogen interference in a J.R. Russell*1, J. Gerardin1, A.L. national survey Ouedraogo1, D.L. Smith2, I. K. Glass*, A. Lal, M. Rodriguez-Barraquer3, M. Kamya4, Kirk, Australian National J. Nankabirwa4, G. Dorsey3, B. University, Australia Greenhouse3, E.A. Wenger1, 1Institute for Disease Modeling, USA, 2University of Washington, USA, 3University of California, USA, 4Makerere University College of Health Sciences, Uganda, 5Infectious Diseases Research Collaboration, Uganda, 6London School of Hygiene and Tropical Medicine, UK 16:50-17:10 [O7.3] A modified model for [O8.3] Estimating recent [O9.3] Common respiratory vector-borne transmission linking tuberculosis transmission from viruses exhibit interlinked vector abundance to human cluster size distributions epidemiological dynamics density E. Brooks-Pollock*1, H.K. Altes2, L. S. Nickbakhsh*1, C. Mair1, L. V.T.R. Aznar*, M. Danon3, A. Pollock4, D. van Matthews1, R. Reeve1, F. Pascual, University of Chicago, USA Sooligen2, J. Davidson5, M. Thorburn2, B. Von Wissmann2, A. Lalor5, 1University of Bristol, UK, Reynolds3, J. McMenamin3, R.N. 2National Institute for Public Health Gunson2, P.R. and the Environment (RIVM), The Murcia1, 1University of Glasgow, Netherlands, 3University of Exeter, UK, 2NHS Greater Glasgow and UK, 4University of Sheffield, UK, Clyde, UK, 3Health Protection 5Public Health England, UK Scotland, UK 17:10-17:30 [O7.4] Connecting the dots of [O8.4] Real-time decision-making [O9.4] Influenza vaccines alter malaria transmission using genetic during emergency disease within- and between-host networks outbreaks bacterial pathogen dynamics via B. Greenhouse*1, M. Hsiang1, T.A. W.J.M. Probert*1 ,8, C.P. Jewell2, M. generalized herd-effects Perkins2, S. Tessema1, R. Nielsen3, Werkman3, C.J. Fonnesbeck4, M.C. M.J. Mina*1, J.A. McCullers2, R. M. Makame4, A. Schwartz1, M. Runge6, S. Sekiguchi5, K. Shea7, M.J. Antia3, K.P. Klugman3, 1Harvard Murphy1, J. Kemere1, K. Keeling1, M.J. Ferrari7, M.J. Medical School, USA, 2St. Jude Baltzell1, 1University of California Tildesley1, 1University of Warwick, Children's Research Hospital, San Francisco, USA, 2University of UK, 2Lancaster University, UK, USA, 3Emory University, USA, Notre Dame, USA, 3University of 3Imperial College London, UK, 4Emory University, USA California Berkeley, USA, 4Zanzibar 4Vanderbilt University, USA, malaria elimination program, 5University of Miyazaki, Japan, 6US , 5Karolinska Institute, Geological Survey, USA, 7The Sweden, 6University of Namibia, Pennsylvania State University, USA, Namibi 8University of Oxford, UK

Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

17:30-17:50 [O7.5] Tracking malaria by its [O8.5] Integrating multiple data [O9.5] The role of host shadows: Using serology to streams for early outbreak community composition in reconstruct malaria transmission detection: A graph approach Chagas disease transmission I. Rodriguez-Barraquer*1, K. A. Cori1, P. Nouvellet*1, T. Garske1, cycles Tetteh3, I. Ssewanyana2, C. H. Bourhy2, E. Nakouné3, T. D. Erazo*1, J. Cordovez1, C. Drakeley3, B. Jombart1, 1Imperial College Cabrera2, J. Calzada3, A. Saldaña3, Greenhouse1, 1University of London, UK, 2Institut Pasteur, N. Gottdenker2, 1BIOMAC, California, USA, 2Infectious Disease France, 3Institut Pasteur de Baugui, Universidad de los Andes, Research Collaboration, Uganda, Central African Republic Colombia, 2University of Georgia, 3London School of Hygiene and USA, 3Instituto Commemorativo Tropical Medicine, UK Gorgas de Estudios de la Salud, Panama 17:50-19:30 Poster Session 2 I Tramuntana 1 and Foyer Thursday, 30th November 2017 Room Tramuntana II/III Session Chair: TBC 08:30-09:10 [PL05] Friend or foe?: Protection and enhancement mediated by immune responses to Dengue and Zika viruses Eva Harris, University of California Berkeley, USA 09:10-09:50 [PL06] Diversity of immune repertoires Aleksandra Walczak, Ecole Normale Supérieure, France 09:50-10:30 [PL07] Simon Cauchemez, Institute Pasteur, France 10:30-11:00 Refreshment Break I Hall Tramuntana Rooms Tramuntana II/III Mestral Garbi 11:40-12:40 Session 10: Phylodynamics Session 11: Zika Session 12: Epidemics Session Chair: TBC Session Chair: TBC Session Chair: TBC 11:00-11:20 [O10.1] Reconstruction of disease [O11.1] Genomic epidemiology [O12.1] Modelling arboviral transmissions from viral reveals epidemic dynamics of Zika disease epidemics in the Pacific quasispecies genomic data virus in the Caribbean and U.S. islands P. Skums*1 ,2, A. Zelikovsky1, R. Virgin Islands C. Champagne*1 ,2, B. Cazelles1 Singh2, Z. Dimitrova2, S. A. Black*1 ,2, B. Potter2, G. Dudas2, ,3, 1Eco-evolutionary Ramachandran2, D. Campo2, D. L.R. Feldstein2, M.E. Halloran1 ,2, mathematic, IBENS, France, Jha2, L. Bunimovich3, E. N.D. Grubaugh3, K.G. Andersen3, 2CREST, ENSAE, Université Paris Costenbader4, C. Sexton2, 1Georgia B.R. Ellis4, E.M. Ellis4, T. Saclay, France, 3UMMISCO, State University, USA, 2Centers for Bedford2, 1University of UPMC-IRD, France Disease Control and Prevention, Washington, USA, 2Fred Hutchinson USA, 3Georgia Institute of Cancer Research Center, USA, 3The Technology, USA, 4FHI 360, USA Scripps Research Institute, USA, 4U.S. Virgin Islands Department of Health, U.S. Virgin Islands 11:20-11:40 [O10.2] Integrating viral sequence [O11.2] Using serological and [O12.2] Explaining the and epidemiological data to define surveillance data to infer the transmission dynamics of transmission patterns for unobserved transmission dynamics enterovirus serotypes: From respiratory syncytial virus (RSV) of Zika virus in Fiji 2013-2017 regular epidemics to infrequent I.K. Kombe*1 ,2, G.F. Medley2, M. A. Henderson*1, M. Kama2, V.M. outbreaks Baguelin2 ,3, J. Nokes1 ,4, 1KEMRI- Cao-Lormeau3, C. Lau4, J. Edmunds1, M. Pons-Salort*, N.C. Wellcome Trust Research C. Watson1, A. Kucharski1, 1London Grassly, Imperial College London, Programme, , 2London School School of Hygiene & Tropical UK of Hygiene and Tropical Medicine, Medicine, UK, 2Ministry of Health, UK, 3Public Health England, UK, Fiji, 3Institut Louis Malardé, French 4University of Warwick, UK Polynesia, 4University of Queensland, Australia Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

11:40-12:00 [O10.3] Viral phylodynamics using [O11.3] Spread of Zika Virus in the [O12.3] Successive waves of regression-based approximate Americas: A computational human migrations shaped the bayesian computation modelling approach global population structure of E. Saulnier*1 ,2, O. Gascuel2 ,3, S. A. Vespignani*1, Q. Zhang1, K. Sun1, Mycobacterium tuberculosis in Alizon1, 1Laboratoire MIVEGEC A. Pastore y Piontti1, M. Chinazzi1, France (CNRS, IRD, UM), France, 2IBC N.E. Dean2, S. Merler3, L. Rossi4, M. Barbier1 ,2, G. Lina3 ,4, J-P. (LIRMM, CNRS, UM), France, 3C3BI D.P. Rojas2, D. Flandrois4, P. Supply5, T. Wirth*1 (CNRS, Institut Pasteur), France Mistry1, 1Northeastern University, ,2, J-P. Rasigade3 ,4, 1Université USA, 2University of Florida, USA, Pierre et Marie Curie, Sorbonne 3Bruno Kessler Foundation, Italy, Universités, France, 2PSL 4Institute for Scientific Interchange Research University, France, Foundation, Italy, 5Fred Hutchinson 3CIRI, University of Lyon, France, Cancer Research Center, USA, 4Hospices Civils de Lyon, France, 6Bocconi University, Italy 5Center for Infection and Immunity of Lille, France 12:00-12:20 [O10.4] Simulation and inference [O11.4] Combining different data [O12.4] Cholera in 1853: Historic of phylodynamic individual level sources to understand Zika epidemics provide new clues in models outbreaks the fight against an old enemy J. Angevaare*1, Z. Feng1, R. S. Funk*, A.J. Kucharski, O.J. M.D. Phelps*1, M.L. Perner1, V.E. Deardon2, 1University of Guelph, Brady, London School of Hygiene & Pitzer2, P.K.M. Jensen1, V. Canada, 2University of Calgary, Tropical Medicine, UK Andreasen3, L. Canada Simonsen1, 1University of Copenhagen, Denmark, 2Yale University, USA, 3Roskilde University, Denmark 12:20-12:40 [O10.5] Phybreak: A method and [O11.5] Inferring the risk factors [O12.5] Characterizing R-package to reconstruct behind the geographical spread infectious diseases threats using transmission trees with sequence and transmission of Zika in the epidemic doubling times data Americas G. Chowell*1 ,2, L. DeCamp1, C. D. Klinkenberg*1, C. Colijn2, X. L.M. Gardner*1, A. Bota1, N.D. Viboud2, 1Georgia State Didelot2, J. Wallinga1 ,3, 1National Grubaugh2, K. Gangavarapu2, University, USA, 2National Institute for Public Health and the M.U.G. Kraemer3 ,4, 1UNSW Sydney, Institutes of Health, USA Environment, The Netherlands, Australia, 2Scripps Research 2Imperial College London, UK, Institute, USA, 3University of Oxford, 3Leiden University Medical Centre, UK, 4Boston Children’s Hospital, The Netherlands USA, 5Harvard Medical School, USA 12:40-14:00 Lunch I Noray Restaurant Rooms Tramuntana II/III Mestral Garbi 14:00-16:00 Session 13: Dengue Session 14: Statistical methods Session 15: Vaccination Session Chair: TBC Session Chair: TBC Session Chair: TBC 14:00-14:20 [O13.1] Mapping global variation [O14.1] Confronting uncertainty: [O15.1] The polio ‘end game’ in dengue transmission intensity Bayesian analytics and simulation challenge – eradicating a and assessing the impact of to support the Zika epidemic vaccine: Spatial and temporal control strategies response dynamics of type-2 vaccine L. Cattarino*1, I. Rodríguez- M.A. Johansson*1 ,2, L. Mier-y- poliovirus detection in stool and Barraquer2, D.A.T. Cummings3, N. Teran1, D.M. Rodriguez1, J.M. sewage following global Imai1, N.M. Ferguson1, 1Imperial Healy1, B.R. Greening Jr.1, S.P. withdrawal in April 2016 College London, UK, 2Johns Hopkins Russell1, T.M. Quandelacy1 I.M. Blake*, M. Pons-Salort, N. University, USA, 3University of ,3, 1Center for Disease Control and Molodecky, N.C. Florida, USA Prevention, USA, 2Harvard TH Chan Grassly, Imperial College School of Public Health, USA, 3Johns London, UK Hopkins Bloomberg School of Public Health, USA 14:20-14:40 [O13.2] Antibody titer dynamics [O14.2] A novel Bayesian [O15.2] Vaccination-induced provide insight into dengue geostatistical method for immunity versus antigenic disease risk estimating tuberculosis incidence distance in the transmission Antibody titer dynamics provide reveals many missed TB cases in dynamics of H5N1 influenza insight into dengue disease risk Ethiopia viruses H. Salje*1 ,2, D.A.T. Cummings3 ,2, I. D. Shaweno*1 ,3, J.M. Trauer1 ,2, J.T. I. Sitaras*1 ,2, B. Peeters2, M.C.M. Rodriguez-Barraquer4, 1Institut Denholm3 ,4, E.S. McBryde1 de Jong1, 1Wageningen Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

Pasteur, France, 2Johns Hopkins, ,5, 1University of Melbourne, University and Research, The USA, 3University of Florida, USA, Australia, 2Monash University, Netherlands, 2Wageningen 4UCSF, USA Australia, 3Victorian Tuberculosis Bioveterinary Research, The Program at the Peter Doherty Netherlands Institute for Infection and Immunity, Australia, 4University of Melbourne, Australia, 5James Cook University, Australia 14:40-15:00 [O13.3] Characterizing the extent [O14.3] The R Epidemics [O15.3] Model-based and impact of dengue antigenic Consortium: Building the next projections of Zika virus diversity generation of statistical tools for infections to inform vaccine trial S.M. Bell*1 ,2, T. Bedford1, 1Fred outbreak response using R site selection Hutch Cancer Research Center, T. Jombart, Imperial College T.A. Perkins*1, A.S. Siraj1, S.M. USA, 2University of Washington, London, UK Moore1, C.M. Barker2, R.C. USA Reiner3, 1University of Notre Dame, USA, 2University of California, USA, 3University of Washington, USA 15:00-15:20 [O13.4] Transmission-recovery [O14.4] Using ensemble models to [O15.4] A method to quantify trade-offs indicate that dengue predict outbreaks of vector-borne the impact of changes to an virulence evolution depends on disease immunisation programme: epidemiological context A.L. Buczak*, B. Baugher, L. Moniz, Illustrative application to the UK R. Ben-Shachar*1, K. Koelle2, 1UC S. Babin, Johns Hopkins University routine childhood vaccine Berkeley, USA, 2Emory University, APL, USA schedule USA, 3Duke University, USA J. Panovska-Griffiths*1 ,2, S. Crowe1, C. Pagel1, G. Walker3, G. Wooton3, P. Grove3, M. Utley1, 1University College London, UK, 2London School of Hygiene and Tropical Medicine, UK, 3Department of Health, UK 15:20-15:40 [O13.5] Disentangling the relative [O14.5] Modelling outbreaks with [O15.5] Harnessing big data to roles of environmental conditions a sub-exponential branching quantify vaccine hesitancy and and importation in driving process the erosion of herd immunity interannual variation in dengue A.E. Zarebski*1, R. Moss1, P. S. Goldlust, epidemics in Guangzhou, China Dawson3, J.M. McCaw1 ,2, 1The S.Bansal*, Georgetown R.J. Oidtman*1, Z. Huang2, S. Lai2 ,3, University of Melbourne, Australia, University, USA Y. Li2, R.C. Reiner4, A.J. Tatem3 ,5, H. 2Murdoch Childrens Research Yu2, T.A. Perkins1, 1University of Institute, Australia, 3Defence Notre Dame, USA, 2Center for Science and Technology Group, Disease Control and Prevention, Australia China, 3University of Southampton, UK, 4University of Washington, USA, 5Flowminder Foundation, Sweden 15:40-16:00 [O13.6] Refining the [O14.6] Scalable inference for [O15.6] Containing Ebola at the characterization of a live epidemic models with individual source with vaccination strategies attenuated tetravalent dengue level data M. Ajelli*1 ,2, S. Merler2, K. Sun1, vaccine's efficacy profile using S.E.F. Spencer*, P. Touloupou, B. L. Fumanelli2, S. Parlamento2, A. machine learning Finkenstadt Rand, University of Pastore y Piontti1, M. Chinazzi1, I. Dorigatti*1, C.A. Donnelly1, D. Warwick, UK N.E. Dean3, G. Putoto4, D. Laydon1, R. Small2, N. Jackson3, L. Carraro4, 1Northeastern Coudeville3, N.M. University, USA, 2Bruno Kessler Ferguson1, 1Imperial College Foundation, Italy, 3University of London, UK, 2Sanofi Pasteur, USA, Florida, USA, 4Doctors with Africa 3Sanofi Pasteur, France – CUAMM, Italy 16:00-16:20 Refreshment Break I Hall Tramuntana

Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

Rooms Tramuntana II/III Mestral Garbi 16:20-17:40 Session 16: AMR 2 Session 17: Influenza serology Session 18: Control Session Chair: TBC Session Chair: TBC Session Chair: TBC 16:20-16:40 [O16.1] Using models to understand [O17.1] Structure of general- [O18.1] Modelling the potential how molecular mechanisms of population antibody titer of ivermectin treated cattle as a resistance affect the risk of acquired distributions to influenza A virus novel malaria vector control drug resistance during treatment N.T.D. Nguyen*1 ,6, S. Todd1 ,2, M.F. tool: Implications of killing F. Clarelli*1, L. Chindelevitch2, B. Boni1 ,3, E. de Bruin4 ,5, M. zoophilic mosquitoes Singh1, T. Cohen3, S. Abel1, P. Abel zur Koopmans4 ,5, H.T.V. Nguyen1, T.N.T. A. Dighe*, A. Ghani, H. Wiesch1, 1UiT Arctic University of Tran1, T.L.T. Nguyen1, V.V.C. Slater, Imperial College London, , Norway, 2Simon Fraser Nguyen1, S. Baker1 ,6, 1Oxford UK University, Canada, 3Yale School of University Clinical Research Unit, Public Health, USA Viet Nam, 2Liverpool School of Tropical Medicine, UK, 3Pennsylvania State University, USA, 4Erasmus Medical Centre, The Netherlands, 5National Institute for Public Health and the Environment, The Netherlands, 6University of Oxford, UK 16:40-17:00 [O16.2] Estimating the proportion of [O17.2] Uncovering the [O18.2] Achieving global goals bystander selection for antibiotic epidemiological and immunological for schistosomiasis: Rapidly resistance in the US dynamics of influenza from reaching the 2020 and 2025 C. Tedijanto*1, S. Olesen1, C. serological data goals for control and elimination Huttenhower1, Y. Grad1 ,2, M. A.J. Kucharski*1, J. Lessler2, D.A.T. of morbidity Lipsitch1, 1Harvard T.H. Chan School Cummings3, S. Riley4, 1London A.K. Deol*1 ,2, F. Fleming1, B. of Public Health, USA, 2Brigham and School of Hygiene & Tropical Calvo-Urbano1, 1Imperial College Women's Hospital, Harvard Medical Medicine, UK, 2Johns Hopkins London, UK, 2Schistosomiasis School, USA University, USA, 3University of Control Initiative, UK, 3Royal Florida, USA, 4Imperial College Veterinary College, UK, 4Ministry London, UK of Health Burundi, Burundi, 5Ministry of Health Niger, Niger, 6Ministry of Health Uganda, Uganda, 7Ministry of Health Malawi, Malawi, 8Ministry of Health Tanzania, Tanzania, 9Ministry of Health Yemen, Yemen 17:00-17:20 [O16.3] How competition shapes the [O17.3] Serological measures of [O18.3] Wormy households: dynamics of antimicrobial resistance influenza incidence in the presence Modelling and inference of soil- T.C.M. Dewé*1, C. Fraser2, N.J. of secular trends in exposure and transmitted helminthiasis Croucher1, 1Imperial College London, immuno-modulation of response transmission dynamics UK, 2University of Oxford, UK T.M. Quandelacy*1, D.A.T. A. Bishop*1, C. Holland2, T. Cummings1 ,2, C.Q. Jiang3, K.O. House3, T.D. Kwok4, S. Ruiyin3, J.M. Read5, H. Zhu6 Hollingsworth1, 1University of ,7, Y. Guan6 ,7, S. Riley8, J. Warwick, UK, 2Trinity College, Lessler1, 1Johns Hopkins Bloomberg Ireland, 3University of School of Public Health, USA, Manchester, UK 2University of Florida, USA, 3Guangzhou No. 12 Hospital, China, 4Chinese University of Hong Kong, Hong Kong, 5Lancaster Medical School, Lancaster University, UK, 6University of Hong Kong School of Public Health, Hong Kong, 7Shantou University Medical College, China, 8Imperial College London, UK 17:20-17:40 [O16.4] Mechanisms that maintain [O17.4] Forecasting future influenza [O18.4] Characteristics of Ebola coexistence of antibiotic sensitivity seasons: The importance of virus disease transmission in and resistance also promote high serology Guinea: Impact of the Ebola ça frequencies of multi-drug resistance E. van Leeuwen*1 ,2, K. Hoschler1, R. Suffit trial Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

S. Lehtinen*1, J. Lees4, F. Blanquart2, Pebody1, M. Zambon1, S. Riley2, M. A. Robert1, W.J. Edmunds1, C.H. N. Croucher2, S. Bentley4, P. Turner5, Baguelin1 ,3, 1Public Health England, Watson1, A.M. Henao-Restrepo2, M. Lipsitch2, C. Fraser1, 1University of UK, 2Imperial College London, UK, P.S. Gsell2, I.M. Longini2 ,3, A.J. Oxford, UK, 2Imperial College London, 3London School of Hygiene and Kucharski1, R.M. UK, 3Harvard University, USA, Tropical Medicine, UK Eggo*1, 1London School of 4Wellcome Trust Genome Campus, Hygiene & Tropical Medicine, UK, UK, 5Angkor Hospital for Children, 2WHO, Switzerland, 3University of Cambodia Florida, USA 17:40-19:20 Poster Session 3 I Tramuntana 1 and Foyer 19:30-22:00 Conference Dinner – Ticket holders only Location: TBC Friday, 1st December 2017 Room Tramuntana II/III | Session Chair: TBC 08:30-09:10 [PL08] Christl Donnelly Imperial College London, UK 09:10-09:50 [PL09] The RAPIDD Ebola forecasting challenge: Synthesis and lessons Learnt Cecile Viboud, Fogarty International Center, USA 09:50-10:20 Refreshment Break I Hall Tramuntana Rooms Tramuntana II/III Mestral Garbi 10:20-12:00 Session 19: Spatial and related Session 20: Within host Session 21: Influenza 2 structure Session Chair: TBC Session Chair: TBC Session Chair: TBC 10:20-10:40 [O19.1] Image-based, network [O20.1] Using sequential infection [O21.1] Influenza A virus models of pathogens’ spatial experiments to quantify innate and transmission bottleneck size spread adaptive immunity during influenza estimation from viral deep- G.A. Almogy*, L.S. Stone, RMIT infection sequencing data University, Australia A.W.C. Yan*1, S.G. Zaloumis1, J.A. A.S. Leonard*1 ,2, D. Weissman3, B. Simpson1, J.M. McCaw1 ,2, 1The Greenbaum4, E. Ghedin5, K. Koelle1 University of Melbourne, Australia, ,3, 1Duke University, USA, 2Duke 2Murdoch Childrens Research University School of Medicine, USA, Institute, Australia 3Emory University, USA, 4Icahn School of Medicine at Mount Sinai, USA, 5New York University, USA 10:40-11:00 [O19.2] Unravelling the spatial [O20.2] Using a mathematical model [O21.2] Reconstructing the pattern of the chikungunya virus to optimally select a live attenuated antigenic evolution of influenza emergence in the Martinique influenza vaccine A/H3 viruses in multiple hosts Island: Implications for the L. Matrajt*1, M.E. Halloran1 ,2, R. N.S. Trovao*1 ,2, M.I. Nelson2, T. management of emerging Antia3, 1Fred Hutchinson Cancer Bedford3, P. Lemey4, 1Icahn School arboviruses Research Center, USA, 2University of of Medicine at Mount Sinai, USA, T. Vergne*1, B. Cazelles2, M. Washington, USA, 3Emory University, 2Fogarty International Center, Etienne3, B. Roche1, 1Institut de USA National Institutes of Health, USA, Recherche pour le Développement, 3Vaccine and Infectious Disease France, 2Ecole Normale Division, Fred Hutchinson Cancer Supérieure, France, 3Collectivité Research Center, USA, 4University of Territoriale de Martinique, France Leuven, Belgium 11:00-11:20 [O19.3] Geospatial Characteristics [O20.3] Infectious reactivation of [O21.3] Contrasting the geographic of Measles Transmission in China cytomegalovirus explaining age- and transmission of seasonal and during 2005−2014 sex-specific patterns of pandemic influenza in the United W. Yang*1, L. Wen2, S-L. Li1, K. seroprevalence States using a gravity-based model Chen3, W-Y. Zhang2, J. M. van Boven*1, J. van de Kassteele1, S.M. Kissler*1, C. Viboud2, V. Shaman1, 1Columbia University, M.J. Korndewal1 ,2, C.H. van Dorp1 ,3, Charu3, O.N. Bjørnstad4, L. USA, 2Academy of Military Medical M. Kretzschmar1, F. van der Klis1, H.E. Simonsen5, B.T. Grenfell6, J.R. Sciences, China, 3Nanjing de Melker1, A.C. Vossen2, 1National Gog1, 1University of Cambridge, University, China Institute for Public Health, The UK, 2National Institutes of Health, Netherlands, 2Leiden University USA, 3Johns Hopkins Bloomberg Medical Center, The Netherlands, School of Public Health, USA, 3Utrecht University, The Netherlands 4Pennsylvania State University, USA, 5University of Copenhagen, Denmark, 6Princeton University, Epidemics6 - International Conference on Infectious Disease Dynamics 2017 | Oral Programme

USA 11:20-11:40 [O19.4] Extending household [O20.4] Understanding the measles [O21.4] Minimum-path work- models to endemic settings paradox: Modeling the impact of commute distance and the spatial J.B. Hilton*, M.J. viral infection on the host immune spread of influenza Keeling, University of Warwick, system V. Charu1, S. Zeger2, J. Gog3 ,1, O. UK S.E. Morris*1, A.N. Nelson2, R.D. Bjornstad4 ,1, S. Kissler3, L. Kouyos3, W-H. Lin4, M.J. Mina5, R.L. Simonsen5 ,1, B. Grenfell6 ,1, C. de Swart6, A.J. Yates7, D.E. Griffin2, Viboud*1, 1National Institutes of B.T. Grenfell1, 1Princeton University, Health, USA, 2Johns Hopkins USA, 2Johns Hopkins University, USA, University, USA, 3University of 3University Hospital Zurich, Cambridge, UK, 4Pennsylvania State Switzerland, 4Columbia University, University, USA, 5Copenhagen USA, 5Harvard Medical School, USA, University, Denmark, 6Princeton 6Erasmus Medical Center, The University, USA Netherlands, 7University of Glasgow, UK 11:40-12:00 [O19.5] The effects of [O20.5] Capturing the roles of [O21.5] Integrating dynamical metapopulation structure on cellular coinfection and viral modelling and phylogeographic fine-scale mosquito population complementation in the within-host inference to uncover the drivers of dynamics and potential dynamics of influenza global influenza circulation consequences for the K. Koelle*1, R. Ke2, C. C. Poletto*1, T. Bedford2, M. transmission dynamics of dengue Brooke3, 1Emory University, USA, Suchard3, V. Colizza1 ,4, P. and malaria 2North Carolina State University, USA, Lemey5, 1INSERM, France, 2Fred C. McCormack*, A.C. Ghani, N.M. 3University of Illinois at Urbana- Hutchinson Cancer Research Center, Ferguson, Imperial College Champaign, USA USA, 3University of California, USA, London, UK 4ISI Foundation, Italy, 5University of Leuven, Belgium 12:00:12:20 Refreshment Break I Hall Tramuntana Room Tramuntana II/III | Session Chair: TBC 12:20-13:00 [PL10] Derek Cummings | University of Florida, USA 13:00-13:20 Conference Closing