Comparing the transmission potential from sequence and surveillance data of 2009 North American influenza pandemic waves

作     者：Venkata R.Duvvuri Joseph T.Hicks Lambodhar Damodaran Martin Grunnill Thomas Braukmann Jianhong Wu Jonathan B.Gubbay Samir N.Patel Justin Bahl 

作者机构：Public Health OntarioTorontoOntarioCanada Department of Laboratory Medicine and PathobiologyFaculty of MedicineUniversity of TorontoTorontoOntarioCanada Laboratory for Industrial and Applied MathematicsDepartment of Mathematics and StatisticsYork UniversityTorontoOntarioCanada Center for the Ecology of Infectious DiseaseDepartment of Infectious DiseasesInstitute of BioinformaticsUniversity of GeorgiaAthensGeorgia Department of Epidemiology and BiostatisticsInstitute of BioinformaticsUniversity of GeorgiaAthensGeorgia Duke-NUS Graduate Medical SchoolSingapore 

出 版 物：《Infectious Disease Modelling》 (传染病建模（英文）)

年 卷 期：2023年第8卷第1期

页      面：240-252页

核心收录：

学科分类：1004[医学-公共卫生与预防医学(可授医学、理学学位)] 100401[医学-流行病与卫生统计学] 10[医学] 

基　　金：National Institutes of Health(NIH)Centers for Excellence in Influenza Research and Surveillance(contract#HHSN272201400006C) National Institute of Allergy and Infectious Diseases,National Institutes of Health,Department of Health and Human Services,under Contract No.75N93021C00018(NIAID Centers of Excellence for Influenza Research and Response,CEIRR) 

主　　题：Phylodynamics Pandemic 2009 H1N1 Reproduction number Coalescent growth models Birth-death models Pathogen sequence data Public health 

摘      要：Technological advancements in phylodynamic modeling coupled with the accessibility of real-time pathogen genetic data are increasingly important for understanding the infectious disease transmission *** this study,we compare the transmission potentials of North American influenza A(H1N1)pdm09 derived from sequence data to that derived from surveillance *** impact of the choice of tree-priors,informative epidemiological priors,and evolutionary parameters on the transmission potential estimation is *** American Influenza A(H1N1)pdm09 hemagglutinin(HA)gene sequences are analyzed using the coalescent and birth-death tree prior models to estimate the basic reproduction number(R_(0)).Epidemiological priors gathered from published literature are used to simulate the birth-death skyline ***-sampling marginal likelihood estimation is conducted to assess model fit.A bibliographic search to gather surveillancebased R_(0)values were consistently lower(mean≤1.2)when estimated by coalescent models than by the birth-death models with informative priors on the duration of infectiousness(mean≥1.3 to≤2.88 days).The user-defined informative priors for use in the birth-death model shift the directionality of epidemiological and evolutionary parameters compared to non-informative *** there was no certain impact of clock rate and tree height on the R_(0)estimation,an opposite relationship was observed between coalescent and birth-death tree *** was no significant difference(p=0.46)between the birth-death model and surveillance R0 *** study concludes that treeprior methodological differences may have a substantial impact on the transmission potential estimation as well as the evolutionary *** study also reports a consensus between the sequence-based R_(0)estimation and surveillanceased R_(0)***,these outcomes shed light on the potential role of phylodynamic modeling to augment existing surveillance