title: Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.
abstract: Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd.
authors.affiliation: Department of Statistics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
authors.forename: Gabriela B
authors.initials: GB
authors.lastname: Cybis
authors.affiliation: Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.|Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.|Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California, U.S.A.
authors.forename: Janet S
authors.initials: JS
authors.lastname: Sinsheimer
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A.
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Edinburgh, U.K.|Fogarty International Center, National Institutes of Health, Bethesda, Maryland, U.S.A.
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.affiliation: Department of Microbiology and Immunology, Rega Institute, University of Leuven, Leuven, Belgium.
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.affiliation: Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.|Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, U.S.A.|Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, California, U.S.A.
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
mesh_terms: D000956:Antigens, Viral / Q000235:genetics* / Q000276:immunology*; D001499:Bayes Theorem; D056808:Biostatistics; D016000:Cluster Analysis; D019143:Evolution, Molecular; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics / Q000276:immunology; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology*; D016013:Likelihood Functions; D008957:Models, Genetic; D018448:Models, Immunological; D017720:Molecular Epidemiology; D010802:Phylogeny; D018709:Statistics, Nonparametric; D013269:Stochastic Processes
chemical_list: D000956:Antigens, Viral
keywords: Bayesian nonparametric mixture models; antigenic cartography; phylodynamics