FluHMM: a simple and flexible Bayesian algorithm for sentinel influenza surveillance and outbreak detection

Theodore Lytras, Kassiani Gkolfinopoulou, Stefanos Bonovas, Baltazar Nunes

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


Timely detection of the seasonal influenza epidemic is important for public health action. We introduce FluHMM, a simple but flexible Bayesian algorithm to detect and monitor the seasonal epidemic on sentinel surveillance data. No comparable historical data are required for its use. FluHMM segments a typical influenza surveillance season into five distinct phases with clear interpretation (pre-epidemic, epidemic growth, epidemic plateau, epidemic decline and post-epidemic) and provides the posterior probability of being at each phase for every week in the period under surveillance, given the available data. An alert can be raised when the probability that the epidemic has started exceeds a given threshold. An accompanying R package facilitates the application of this method in public health practice. We apply FluHMM on 12 seasons of sentinel surveillance data from Greece, and show that it achieves very good sensitivity, timeliness and perfect specificity, thereby demonstrating its usefulness. We further discuss advantages and limitations of the method, providing suggestions on how to apply it and highlighting potential future extensions such as with integrating multiple surveillance data streams.

Original languageEnglish
Pages (from-to)1826-1840
JournalStatistical Methods In Medical Research
Issue number6
Publication statusPublished - 2019


  • Bayesian statistics
  • disease surveillance
  • epidemics
  • hidden Markov model
  • Influenza
  • outbreak detection
  • seasonal influenza


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