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Triggering Interventions for Flu: The ALERT Algorithm

Nicholas G Reich
December 10, 2015
120

Triggering Interventions for Flu: The ALERT Algorithm

Presentation made at the International Society for Disease Surveillance conference describing the ALERT algorithm, a method for predicting the onset of influenza season.

Nicholas G Reich

December 10, 2015
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Transcript

  1. Triggering Interventions for Flu:
    The ALERT Algorithm
    Nicholas G Reich
    Department of Biostatistics and Epidemiology
    University of Massachusetts - Amherst
    10 Dec 2015 :: ISDS :: Denver, CO
    @reichlab
    http://reichlab.github.io

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  2. Anecdote:
    triggering the ResPECT
    Study intervention period
    in 2012-2013

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  3. The ResPECT Study
    Cluster-randomized clinical trial
    comparing N95 respirators vs. surgical
    masks at preventing respiratory
    infections in healthcare workers.

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  4. How to decide when
    to start the ResPECT
    study each season?
    12 week “active” study period,
    ideally covering the peak flu season

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  5. 0
    20
    40
    60
    80
    100
    120
    ODEïFRQILrPHG)OX$FDVHV
    200
    300
    ILrPHG)OX$FDVHV
    Johns Hopkins Hospital
    &KLOGUHQ·V+RVSLWDO&RORUDGR
    0
    20
    40
    60
    80
    100
    120
    ODEïFRQILrPHG)OX$FDVHV
    0
    100
    200
    300
    ODEïFRQILrPHG)OX$FDVHV
    2002 2003 2004 2005 2006 2007 2008 2009 2010
    Johns Hopkins Hospital
    &KLOGUHQ·V+RVSLWDO&RORUDGR
    Data from one ResPECT site: Johns Hopkins

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  6. Johns Hopkins Hospital
    lab-confirmed Influenza A cases

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  7. the “ALERT threshold”
    based on past data, set to 3 cases

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  8. week ending Nov 3 has 3 cases
    (we receive data on Nov 6)

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  9. Recommended start date: Nov 19

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  10. View Slide

  11. View Slide

  12. More generally:
    how to predict when
    flu season is starting?
    Literally, a $75,000 question, according to the CDC.

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  13. Why predict the flu?
    • For clinical trials, to time interventions.

    • In hospitals, to 

    - start target screening for flu antiviral use,

    - limit patient visitation, 

    - increase mandatory PPE usage.

    • For public health agencies, to determine the best
    timing for seasonal risk communication.
    “Predictions that give rise to actionable items that would not
    otherwise occur are important.” - Jay Varma, NYC DOHMH

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  14. The
    Above
    Local
    Elevated
    Respiratory illness
    Threshold
    Algorithm
    Reich et al, Clinical Infectious Diseases, 2015.
    http://tiny.cc/alertapp

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  15. Data Results Choice of
    threshold
    0
    20
    40
    60
    80
    100
    120
    ODEïFRQILrPHG)OX$FDVHV
    0
    100
    200
    300
    ODEïFRQILrPHG)OX$FDVHV
    2002 2003 2004 2005 2006 2007 2008 2009 2010
    Johns Hopkins Hospital
    &KLOGUHQ·V+RVSLWDO&RORUDGR
    How ALERT works

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  16. Data Results Choice of
    threshold
    How ALERT works
    Median  
    dura*on
    Percent  of  cases  captured Peaks  captured Mean  weeks      
    <  threshold
    Mean  dura*on  
    difference
    Threshold median min max % %  +/-­‐  2  
    1 18 96.9 0 99.8 70 70 3.7 3.7
    2 18 97.4 61.3 99.4 90 90 2.9 5.1
    3 15.5 95.6 58 98.7 90 90 1.8 1.8
    4 14.5 94 57.3 98.7 90 80 2 0.8
    5 13 91.8 57.3 96.3 90 80 2.2 -­‐0.3
    6 12.5 90.3 57.3 96.2 90 80 2.6 -­‐0.9
    7 12 86.4 47.7 94.9 80 80 2.7 -­‐1.4
    8 11 82.6 47.7 94.9 80 80 3 -­‐2.1
    9 10.5 82.6 0 94.9 80 60 2.2 -­‐2.44
    10 9 76.8 0 94.9 70 60 2.2 -­‐3.11

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  17. Data Results Choice of
    threshold
    How ALERT works
    Median  
    dura*on
    Percent  of  cases  captured Peaks  captured Mean  weeks      
    <  threshold
    Mean  dura*on  
    difference
    Threshold median minimu
    m
    maximu
    m
    % %  +/-­‐  2  
    1 18 96.9 0 99.8 70 70 3.7 3.7
    2 18 97.4 61.3 99.4 90 90 2.9 5.1
    3 15.5 95.6 58 98.7 90 90 1.8 1.8
    4 14.5 94 57.3 98.7 90 80 2 0.8
    5 13 91.8 57.3 96.3 90 80 2.2 -­‐0.3
    6 12.5 90.3 57.3 96.2 90 80 2.6 -­‐0.9
    7 12 86.4 47.7 94.9 80 80 2.7 -­‐1.4
    8 11 82.6 47.7 94.9 80 80 3 -­‐2.1
    9 10.5 82.6 0 94.9 80 60 2.2 -­‐2.44
    10 9 76.8 0 94.9 70 60 2.2 -­‐3.11

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  18. Data Results Choice of
    threshold
    How ALERT works
    apply ALERT threshold
    to real-time data

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  19. What ALERT is
    • Threshold-based algorithm for surveillance data
    to give early warning signal for epidemic onset.
    • Simple method with cross-validated
    performance assessment.
    • A free online tool for hospital epidemiologists
    and public health officials.
    • Open-source, “beta” software (R package).

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  22. What ALERT is not
    • A statistical prediction model. (not yet…)
    • Generalizable for non-seasonal data.
    • A method for detecting outbreaks of emerging
    pathogens.

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  23. – statistical proverb
    “The plural of anecdote is not data.”

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  24. Region (CDC #) ResPECT Site
    ALERT
    Threshold
    start date/
    season
    % of Flu A
    cases captured
    in 12 weeks
    Northeast (2) NYC VA 19 12/3/2012 94%
    12/16/2013 76%
    12/15/2014 90%
    Mid-Atlantic (3) JHU/DC VA 3 11/19/2012 91%
    12/30/2013 90%
    12/8/2014 95%
    Southwest (8) CHCO/DH 3 12/3/2012 87%
    12/2/2013 93%
    12/1/2014 97%
    South (6) Houston VA 5 11/11/2013 90%
    Data and Results

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  25. The future of ALERT
    [statistics] 

    Incorporate non-parametric prediction model.
    [epidemiology] 

    Apply ALERT to other seasonal diseases.
    [software] 

    Continue development and support of web applet
    and open-source R package.

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  26. Stephen A Lauer
    The ResPECT Study team
    Acknowledgments
    Alexandria C Brown
    Data collection teams/labs
    CHCO, NYC DOHMH,
    JHH, Houston

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  27. Thanks!
    !
    http://tiny.cc/alertapp

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