title: Sequence-based antigenic change prediction by a sparse learning method incorporating co-evolutionary information.
abstract: Rapid identification of influenza antigenic variants will be critical in selecting optimal vaccine candidates and thus a key to developing an effective vaccination program. Recent studies suggest that multiple simultaneous mutations at antigenic sites accumulatively enhance antigenic drift of influenza A viruses. However, pre-existing methods on antigenic variant identification are based on analyses from individual sites. Because the impacts of these co-evolved sites on influenza antigenicity may not be additive, it will be critical to quantify the impact of not only those single mutations but also multiple simultaneous mutations or co-evolved sites. Here, we developed and applied a computational method, AntigenCO, to identify and quantify both single and co-evolutionary sites driving the historical antigenic drifts. AntigenCO achieved an accuracy of up to 90.05% for antigenic variant prediction, significantly outperforming methods based on single sites. AntigenCO can be useful in antigenic variant identification in influenza surveillance.
authors.affiliation: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America.
authors.forename: Jialiang
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Statistics, Rutgers University, Piscataway, New Jersey, United States of America.
authors.forename: Tong
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi, United States of America.
authors.forename: Xiu-Feng
authors.initials: XF
authors.lastname: Wan
mesh_terms: D000940:Antigenic Variation / Q000235:genetics*; D000956:Antigens, Viral / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D009980:Influenza A virus / Q000235:genetics / Q000276:immunology*
chemical_list: D000956:Antigens, Viral