Transmission of and susceptibility to seasonal influenza in Switzerland from 2003 to 2015

Axelsen, 2014, Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers, Proc. Natl. Acad. Sci. U.S.A., 111, 9538, 10.1073/pnas.1321656111 Baguelin, 2013, Assessing optimal target populations for influenza vaccination programmes: an evidence synthesis and modelling study, PLoS Med., 10, e1001527, 10.1371/journal.pmed.1001527 Barclay, 2014, Positive network assortativity of influenza vaccination at a high school: implications for outbreak risk and herd immunity, PLOS ONE, 9, e87042, 10.1371/journal.pone.0087042 Bartko, 1966, Approximating the negative binomial, Technometrics, 8, 345, 10.1080/00401706.1966.10490353 Biggerstaff, 2014, Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature, BMC Infect. Dis., 14, 480, 10.1186/1471-2334-14-480 Carpenter, 2017, Stan: a probabilistic programming language, J. Stat. Softw., 76, 1, 10.18637/jss.v076.i01 Cauchemez, 2004, A Bayesian MCMC approach to study transmission of influenza: application to household longitudinal data, Stat. Med., 23, 3469, 10.1002/sim.1912 Chowell, 2006, Transmission dynamics of the great influenza pandemic of 1918 in Geneva, Switzerland: assessing the effects of hypothetical interventions, J. Theor. Biol., 241, 193, 10.1016/j.jtbi.2005.11.026 Chowell, 2007, Estimating the reproduction number from the initial phase of the Spanish flu pandemic waves in Geneva, Switzerland, Math. Biosci. Eng., 4, 457, 10.3934/mbe.2007.4.457 Cori, 2012, Estimating influenza latency and infectious period durations using viral excretion data, Epidemics, 4, 132, 10.1016/j.epidem.2012.06.001 Cromer, 2014, The burden of influenza in England by age and clinical risk group: a statistical analysis to inform vaccine policy, J. Infect., 68, 363, 10.1016/j.jinf.2013.11.013 Fumanelli, 2012, Inferring the structure of social contacts from demographic data in the analysis of infectious diseases spread, PLoS Comput. Biol., 8, e1002673, 10.1371/journal.pcbi.1002673 Goeyvaerts, 2015, Estimating dynamic transmission model parameters for seasonal influenza by fitting to age and season-specific influenza-like illness incidence, Epidemics, 13, 1, 10.1016/j.epidem.2015.04.002 Hancock, 2009, Cross-reactive antibody responses to the 2009 pandemic H1N1 influenza virus, N. Engl. J. Med., 361, 1945, 10.1056/NEJMoa0906453 Heffernan, 2005, Perspectives on the basic reproductive ratio, J. R. Soc. Interface, 2, 281, 10.1098/rsif.2005.0042 Hôpitaux Universitaires Genève, 2017. Centre National de Référence de l’Influenza – CNRI. https://www.hug-ge.ch/laboratoire-virologie/centre-national-reference-influenza-cnri (accessed 24.11.17). Keeling, 2008 Kucharski, 2015, Estimating the life course of influenza A(H3N2) antibody responses from cross-sectional data, PLoS Biol., 13, e1002082, 10.1371/journal.pbio.1002082 Lofgren, 2007, Influenza seasonality: underlying causes and modeling theories, J. Virol., 81, 5429, 10.1128/JVI.01680-06 Lunelli, 2013, Understanding the dynamics of seasonal influenza in Italy: incidence, transmissibility and population susceptibility in a 9-year period, Influenza Other Respir. Viruses, 7, 286, 10.1111/j.1750-2659.2012.00388.x Memoli, 2013, Influenza in pregnancy, Influenza Other Respir. Viruses, 7, 1033, 10.1111/irv.12055 Mossong, 2008, Social contacts and mixing patterns relevant to the spread of infectious diseases, PLoS Med., 5, e74, 10.1371/journal.pmed.0050074 Diekmann, 2013 Prem, 2017, Projecting social contact matrices in 152 countries using contact surveys and demographic data, PLoS Comput. Biol., 13, e1005697, 10.1371/journal.pcbi.1005697 R Core Team, 2015 Rios-Doria, 2009, Qualitative analysis of the level of cross-protection between epidemic waves of the 1918–1919 influenza pandemic, J. Theor. Biol., 261, 584, 10.1016/j.jtbi.2009.08.020 Shaman, 2011, Absolute humidity and pandemic versus epidemic influenza, Am. J. Epidemiol., 173, 127, 10.1093/aje/kwq347 Shaman, 2010, Absolute humidity and the seasonal onset of influenza in the continental United States, PLoS Biol., 8, e1000316, 10.1371/journal.pbio.1000316 Smieszek, 2011, Reconstructing the 2003/2004 H3N2 influenza epidemic in Switzerland with a spatially explicit, individual-based model, BMC Infect. Dis., 11, 115, 10.1186/1471-2334-11-115 Somaini, 1986, Morbidity detection in general practice, Soz Praventivmed., 31, 37, 10.1007/BF02103746 Somes, 2018, Estimating the annual attack rate of seasonal influenza among unvaccinated individuals: a systematic review and meta-analysis, Vaccine, 36, 3199, 10.1016/j.vaccine.2018.04.063 Stan Development Team, 2016. RStan: the R interface to Stan. Version 2.9.0. URL http://mc-stan.org. Swiss Federal Office of Meteorology and Climatology MeteoSwiss, 2017 Swiss Federal Statistical Office, 2017 Tamerius, 2013, Environmental predictors of seasonal influenza epidemics across temperate and tropical climates, PLoS Pathog., 9, e1003194, 10.1371/journal.ppat.1003194 Taubenberger, 2008, The pathology of influenza virus infections, Annu. Rev. Pathol., 3, 499, 10.1146/annurev.pathmechdis.3.121806.154316 Tsang, 2016, Household transmission of influenza virus, Trends Microbiol., 24, 123, 10.1016/j.tim.2015.10.012 Wu, 2014, Inferring influenza infection attack rate from seroprevalence data, PLoS Pathog., 10, e1004054, 10.1371/journal.ppat.1004054 Yuan, 2017, The impact of stratified immunity on the transmission dynamics of influenza, Epidemics, 20, 84, 10.1016/j.epidem.2017.03.003