@article{neher_prediction_2016,
 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.},
 area = {influenza_evolution},
 author = {Neher, Richard A. and Bedford, Trevor and Daniels, Rodney S. and Russell, Colin A. and Shraiman, Boris I.},
 code = {github.com/nextstrain/augur},
 date = {2016-03-07},
 doi = {10.1073/pnas.1525578113},
 issn = {1091-6490 0027-8424},
 journal = {Proceedings of the National Academy of Sciences of the United States of America},
 keywords = {Amino Acid Sequence, antigenic distance, Antigenic Variation/*genetics, Antigens, Viral/genetics/*immunology, Computer Graphics, Computer Simulation, evolution, Evolution, Molecular, Forecasting, Hemagglutinin Glycoproteins, Influenza Virus/genetics/*immunology, Humans, Influenza A Virus, H1N1 Subtype/genetics/*immunology, Influenza A Virus, H3N2 Subtype/genetics/*immunology, Influenza, Human/epidemiology/prevention \& control, Influenza Vaccines, Influenzavirus B/genetics/*immunology, Models, Immunological, Molecular Sequence Data, Phenotype, phylogenetic tree, Phylogeny, Seasons, Software},
 language = {eng},
 month = {March},
 number = {12},
 pages = {E1701--1709},
 pdf = {neher_prediction_2016.pdf},
 pmcid = {PMC4812706},
 pmid = {26951657},
 projectpage = {hi.nextflu.org},
 title = {Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.},
 volume = {113},
 year = {2016}
}