title: Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.
abstract: Human seasonal influenza viruses evolve rapidly, enabling the virus population to evade immunity and reinfect previously infected individuals. Antigenic properties are largely determined by the surface glycoprotein hemagglutinin (HA), and amino acid substitutions at exposed epitope sites in HA mediate loss of recognition by antibodies. Here, we show that antigenic differences measured through serological assay data are well described by a sum of antigenic changes along the path connecting viruses in a phylogenetic tree. This mapping onto the tree allows prediction of antigenicity from HA sequence data alone. The mapping can further be used to make predictions about the makeup of the future A(H3N2) seasonal influenza virus population, and we compare predictions between models with serological and sequence data. To make timely model output readily available, we developed a web browser-based application that visualizes antigenic data on a continuously updated phylogeny.
authors.affiliation: Evolutionary Dynamics and Biophysics, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
authors.forename: Richard A
authors.initials: RA
authors.lastname: Neher
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109;
authors.forename: Trevor
authors.initials: T
authors.lastname: Bedford
authors.affiliation: Worldwide Influenza Centre, The Francis Crick Institute, London NW7 1AA, United Kingdom;
authors.forename: Rodney S
authors.initials: RS
authors.lastname: Daniels
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;
authors.forename: Colin A
authors.identifier: http://orcid.org/0000-0002-2113-162X
authors.initials: CA
authors.lastname: Russell
authors.affiliation: Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106 shraiman@kitp.ucsb.edu.
authors.forename: Boris I
authors.initials: BI
authors.lastname: Shraiman
mesh_terms: D000595:Amino Acid Sequence; D000940:Antigenic Variation / Q000235:genetics*; D000956:Antigens, Viral / Q000235:genetics / Q000276:immunology*; D003196:Computer Graphics; D003198:Computer Simulation; D019143:Evolution, Molecular; D005544:Forecasting; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics / Q000276:immunology*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics / Q000276:immunology*; D053122:Influenza A Virus, H3N2 Subtype / Q000235:genetics / Q000276:immunology*; D007252:Influenza Vaccines; D007251:Influenza, Human / Q000453:epidemiology / Q000517:prevention & control; D029524:Betainfluenzavirus / Q000235:genetics / Q000276:immunology*; D018448:Models, Immunological; D008969:Molecular Sequence Data; D010641:Phenotype; D010802:Phylogeny; D012621:Seasons; D012984:Software
chemical_list: D000956:Antigens, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D007252:Influenza Vaccines
keywords: antigenic distance; evolution; phylogenetic tree