Evolution-informed forecasting of seasonal influenza A (H3N2)

Xiangjun Du, Aaron A. King, Robert J. Woods, Mercedes Pascual
2017 Science Translational Medicine  
Interpandemic or seasonal influenza A, currently subtypes H3N2 and H1N1, exacts an enormous annual burden both in terms of human health and economic impact. Incidence prediction ahead of season remains a challenge largely because of the virus' antigenic evolution. We propose a forecasting approach that incorporates evolutionary change into a mechanistic epidemiological model. The proposed models are simple enough that their parameters can be estimated from retrospective surveillance data. These
more » ... models link amino acid sequences of hemagglutinin epitopes with a transmission model for seasonal H3N2 influenza, also informed by H1N1 levels. With a monthly time series of H3N2 incidence in the United States for more than 10 years, we demonstrate the feasibility of skillful prediction for total cases ahead of season, with a tendency to underpredict monthly peak epidemic size, and an accurate real-time forecast for the 2016/2017 influenza season. RESULTS The monthly incidence variability from 2002 to 2016 for the whole United States is shown in Fig. 1A for reported cases of influenza type A, for subtypes H3N2 and H1N1 (including both seasonal H1N1 and pandemic H1N1), and type B. The time series are computed as the product of the ILI incidence rate, the proportion of ILI samples that tested positive for influenza, the subtype proportion, and the U.S. population size. Thus, incidence data are extrapolated to the U.S. population from outpatients in a network of health care providers, with untyped influenza specimens assigned to H3N2, H1N1, and B, respectively, on the basis of the proportions from the U.S. surveillance system (see Materials and Methods for details). The temporal variability of H3N2 exhibits seasonal outbreaks, whose size varies considerably from one year to the next. This interannual variability can result not only from epidemiological processes such as the loss of immunity to a specific variant of the virus (26) but also to a large degree, from the antigenic evolution of the virus (27) and the combined and complex interactions of the two (28, 29).
doi:10.1126/scitranslmed.aan5325 pmid:29070700 pmcid:PMC5805486 fatcat:rnb346wfmfhmhmkk33l3q5wgdm