Real-time influenza forecasts during the 2012–2013 season

  • Nature Communications 4, Article number: 2837 (2013)
  • doi:10.1038/ncomms3837
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Recently, we developed a seasonal influenza prediction system that uses an advanced data assimilation technique and real-time estimates of influenza incidence to optimize and initialize a population-based mathematical model of influenza transmission dynamics. This system was used to generate and evaluate retrospective forecasts of influenza peak timing in New York City. Here we present weekly forecasts of seasonal influenza developed and run in real time for 108 cities in the USA during the recent 2012–2013 season. Reliable ensemble forecasts of influenza outbreak peak timing with leads of up to 9 weeks were produced. Forecast accuracy increased as the season progressed, and the forecasts significantly outperformed alternate, analogue prediction methods. By week 52, prior to peak for the majority of cities, 63% of all ensemble forecasts were accurate. To our knowledge, this is the first time predictions of seasonal influenza have been made in real time and with demonstrated accuracy.

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Funding was provided by US NIH grant GM100467 (J.S., A.K., W.Y., J.T. and M.L.) and the NIH Models of Infectious Disease Agent Study program through cooperative agreement 1U54GM088558 (J.S., J.T. and M.L.), as well as NIEHS Center grant ES009089 (J.S.) and the RAPIDD program of the Science and Technology Directorate, US Department of Homeland Security (J.S.).

Author information


  1. Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, USA

    • Jeffrey Shaman
    •  & Wan Yang
  2. Climate and Global Dynamics Division, National Center for Atmospheric Research, Boulder, Colorado 80305, USA

    • Alicia Karspeck
  3. Department of Geographical and Sustainability Sciences, University of Iowa, Iowa City, Iowa 52242, USA

    • James Tamerius
  4. Center for Communicable Disease Dynamics, Harvard School of Public Health, Harvard University, Boston, Massachusetts 02115, USA

    • Marc Lipsitch


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J.S., A.K. and M.L. designed the experiments; J.S. performed the experiments and analysis, J.S., A.K., W.Y., J.T. and M.L. interpreted the results and wrote the manuscript.

Competing interests

M.L. discloses consulting or honorarium income from the Avian/Pandemic Flu Registry (Outcome Sciences; funded in part by Roche), AIR Worldwide, Pfizer and Novartis. All other authors declare no competing financial interests.

Corresponding author

Correspondence to Jeffrey Shaman.

Supplementary information

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    Supplementary Information

    Supplementary Figures S1-S10, Supplementary Tables S1-S5, Supplementary Notes 1-2, Supplementary Methods and Supplementary References


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