Journal article

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

John Huddleston, John R Barnes, Thomas Rowe, Xiyan Xu, Rebecca Kondor, David E Wentworth, Lynne Whittaker, Burcu Ermetal, Rodney Stuart Daniels, John W McCauley, Seiichiro Fujisaki, Kazuya Nakamura, Noriko Kishida, Shinji Watanabe, Hideki Hasegawa, Ian Barr, Kanta Subbarao, Pierre Barrat-Charlaix, Richard A Neher, Trevor Bedford

ELIFE | ELIFE SCIENCES PUBLICATIONS LTD | Published : 2020

Abstract

Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecas..

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Awarded by Cancer Research UK


Awarded by Medical Research Council


Awarded by Wellcome


Awarded by Ministry of Health, Labour and Welfare


Awarded by Japan Agency for Medical Research and Development


Awarded by National Institute of Allergy and Infectious Diseases


Awarded by National Institute of General Medical Sciences


Funding Acknowledgements

Cancer Research UK FC001030 Lynne Whittaker Burcu Ermetal Rodney Stuart Daniels John W McCauleyMedical Research Council FC001030 Lynne Whittaker Burcu Ermetal Rodney Stuart Daniels John W McCauleyWellcome FC001030 Lynne Whittaker Burcu Ermetal Rodney Stuart Daniels John W McCauleyMinistry of Health, Labour and Welfare 10110400 Seiichiro Fujisaki Kazuya Nakamura Noriko Kishida Shinji Watanabe Hideki HasegawaJapan Agency for Medical Research and Development JPfk0108118 Shinji WatanabeAustralian Government Department of Health Ian Barr Kanta SubbaraoNational Institute of Allergy and Infectious Diseases F31AI140714 John HuddlestonNational Institute of General Medical Sciences R35GM119774-01 Trevor BedfordPew Charitable Trusts Trevor BedfordNational Institute of Allergy and Infectious Diseases U19AI117891-01 Trevor BedfordNational Institute of Allergy and Infectious Diseases R01AI127893-01 Pierre Barrat-Charlaix Richard A Neher Trevor BedfordThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.