Talk by Sander van Noort on the 1st Symposium of Big Data and Public Health, 2013

1. Influenzanet: ILI monitoring by self-reporting volunteers
Sander van Noort
Instituto Gulbenkian de Ciˆncia, Portugal
e
25 October 2013, Rio de Janeiro
25 October 2013, Rio de Janeiro
Sander van Noort (IGC, Portugal)
Influenzanet
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2. Overview
1
System
2
Comparing ILI surveillance systems
3
Epidemic detection
4
Vaccine efficacy
25 October 2013, Rio de Janeiro
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Influenzanet
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3. Layout
1
System
2
Comparing ILI surveillance systems
3
Epidemic detection
4
Vaccine efficacy
25 October 2013, Rio de Janeiro
Sander van Noort (IGC, Portugal)
Influenzanet
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4. System of Influenzanet
Intake questionnaire
Age
Postal code
Smoking
Vaccination status
Transportation
...
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5. System of Influenzanet
Intake questionnaire
Weekly questionnaire
Age
No symptoms
Postal code
Fever, cough, muscle pain, . . .
Smoking
Vaccination status
Transportation
...
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6. System of Influenzanet
Intake questionnaire
Weekly questionnaire
Age
No symptoms
Postal code
Fever, cough, muscle pain, . . .
Smoking
GP visit
Vaccination status
Stayed home
Transportation
Medicine use
...
...
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7. Europe and other similar systems
2003 (nl, be)
25 October 2013, Rio de Janeiro
Sander van Noort (IGC, Portugal)
Influenzanet
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8. Europe and other similar systems
2003 (nl, be)
2005 (pt)
25 October 2013, Rio de Janeiro
Sander van Noort (IGC, Portugal)
Influenzanet
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9. Europe and other similar systems
2003 (nl, be)
2005 (pt)
2007 (it)
25 October 2013, Rio de Janeiro
Sander van Noort (IGC, Portugal)
Influenzanet
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10. Europe and other similar systems
2003
2005
2007
2009
(nl, be)
(pt)
(it)
(uk)
25 October 2013, Rio de Janeiro
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11. Europe and other similar systems
2003
2005
2007
2009
2011
(nl, be)
(pt)
(it)
(uk)
(se)
25 October 2013, Rio de Janeiro
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12. Europe and other similar systems
2003
2005
2007
2009
2011
2012
(nl, be)
(pt)
(it)
(uk)
(se)
(fr)
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13. Europe and other similar systems
2003
2005
2007
2009
2011
2012
2012
(nl, be)
(pt)
(it)
(uk)
(se)
(fr)
(es)
25 October 2013, Rio de Janeiro
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14. Europe and other similar systems
2003
2005
2007
2009
2011
2012
2012
2013
(nl, be)
(pt)
(it)
(uk)
(se)
(fr)
(es)
(ie)
25 October 2013, Rio de Janeiro
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Influenzanet
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15. Europe and other similar systems
2003
2005
2007
2009
2011
2012
2012
2013
(nl, be)
(pt)
(it)
(uk)
(se)
(fr)
(es)
(ie)
2008
2007
2009
2010
2011
(eu)
(au)
(mx)
(br)
(us)
25 October 2013, Rio de Janeiro
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16. Case definitions
Influenza-like Illness
Fever (at least 38◦ Celsius)
Acute onset
Cough or sore throat
Muscle pain or headache
25 October 2013, Rio de Janeiro
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17. Case definitions
Influenza-like Illness
Fever (at least 38◦ Celsius)
Acute onset
Cough or sore throat
Muscle pain or headache
Common cold
Not ILI, Allergy
Runny or blocked nose;
Sneezing; Cough; Sore
throat (at least 2)
25 October 2013, Rio de Janeiro
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Influenzanet
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18. Case definitions
Influenza-like Illness
Fever (at least 38◦ Celsius)
Acute onset
Cough or sore throat
Muscle pain or headache
Common cold
Not ILI, Allergy
Runny or blocked nose;
Sneezing; Cough; Sore
throat (at least 2)
25 October 2013, Rio de Janeiro
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19. Geographical spread
ILI in the Netherlands/Belgium in 2012/13
25 October 2013, Rio de Janeiro
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20. Participation - Loyalty
Joined in 2003/04
Joined in 2004/05
Joined in 2005/06
Participants
A
Netherlands
B
10000
Joined in 2006/07
Joined in 2007/08
Joined in 2008/09
Belgium
Joined in 2009/10
Joined in 2010/11
C
Portugal
3000
20000
8000
15000
2500
2000
6000
10000
1500
4000
1000
5000
2000
0
0
03/04/05/06/07/08/09/10/
04 05 06 07 08 09 10 11
Season
500
03/04/05/06/07/08/09/10/
04 05 06 07 08 09 10 11
0
06/ 07/ 08/ 09/ 10/
07 08 09 10 11
Season
Season
On average 75% participates again the following season
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21. Layout
1
System
2
Comparing ILI surveillance systems
3
Epidemic detection
4
Vaccine efficacy
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Influenzanet
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22. ILI surveillance systems
Influenzanet
2000
The Netherlands
Influenzanet
ILI / 100,000
1500
1000
500
0
2004
2005
Influenzanet:
2006
2007
2008
Year
2009
2010
2011
2012
2013
Self-reporting volunteers
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23. ILI surveillance systems
Influenzanet
2000
1500
250
200
150
1000
100
Sentinel GPs
ILI / 100,000
Influenzanet
ILI / 100,000
EISN
R2 =0.68
The Netherlands
500
50
0
2004
2005
Influenzanet:
EISN:
2006
2007
2008
Year
2009
2010
2011
2012
2013 0
Self-reporting volunteers
Care-seeking patients
25 October 2013, Rio de Janeiro
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24. ILI surveillance systems
Influenzanet
2000
EISN
Google Flu
The Netherlands
250
Influenzanet
ILI / 100,000
200
150
1000
100
500
50
0
2004
2005
Influenzanet:
EISN:
Google:
2006
2007
2008
Year
2009
2010
2011
2012
Google / Sentinel GPs
ILI / 100,000
1500
2013 0
Self-reporting volunteers
Care-seeking patients
(Online) data mining
25 October 2013, Rio de Janeiro
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25. ILI surveillance systems
Influenzanet
2000
EISN
Google Flu
The Netherlands
250
Influenzanet
ILI / 100,000
200
150
1000
100
500
50
0
2004
2005
Influenzanet:
EISN:
Google:
2006
2007
2008
Year
2009
Self-reporting volunteers
Care-seeking patients
(Online) data mining
2010
2011
2012
Google / Sentinel GPs
ILI / 100,000
1500
2013 0
(FluNearYou, Reporta)
(CDC)
(Twitter, Online news)
25 October 2013, Rio de Janeiro
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26. Reporting bias in Influenzanet
Population
/ Influenzanet
/ ILI
/ Report
9
'
not ILI
ILI Incidence =
ILI
ILI + not ILI
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27. Reporting bias in Influenzanet
Population
/ Influenzanet
/ ILI
/ Report
9
'
not ILI
ILI Incidence =
ILI
ILI + not ILI
Bias: who participates in Influenzanet
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28. Age bias in Influenzanet
Influenzanet
Population
Percentage (%)
120
100
80
60
40
B
20
0
3000
2500
2000
1500
1000
500
0-4
5-14
15-64
0
65+
Nov
Age group
D
C
25
ILI / 100,000
Attack rate (%)
0-4
5-14
15-64
65+
3500
ILI / 100,000
A
20
15
10
Jan
Mar
May
2008 - 2009
Raw
Age corrected
1500
1000
500
5
0
0-4
5-14
15-64
65+
0
Nov
Age group
Jan
Mar
May
2008 - 2009
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29. Reporting bias in EISN
Population
/ Sentinel doctor
/ ILI
ILI Incidence =
/ GP visit
/ Report
GP visits with ILI
Registered patients
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30. Reporting bias in EISN
Population
/ Sentinel doctor
/ ILI
ILI Incidence =
/ GP visit
/ Report
GP visits with ILI
Registered patients
Bias: who visits their GP
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31. GP visits
Sweden
Netherlands
United Kingdom
Portugal
Spain
Italy
France
Belgium
0
20
40
60
80
100
GP visit in 2012/13 with ILI-hist (%)
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32. Age bias in EISN
250
200
150
100
B
C
40
Attack rate (%)
300
0-4
5-14
15-64
65+
GP visit (%)
EISN: ILI / 100,000
A
350
30
20
10
50
0
Oct Dec Feb Apr Jun Aug
2008 - 2009
0
0-4
5-14 15-64 65+
Age group
Raw
Corrected
8
6
4
2
0
0-4
5-14 15-64 65+
Age group
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33. Reporting bias in Google
Population
/ Google
/ ILI
/ Search
9
%
not ILI
ILI Incidence = Function(ILI searches)
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34. Reporting bias in Google
Population
/ Google
/ ILI
/ Search
9
%
not ILI
ILI Incidence = Function(ILI searches)
Bias: Does an ILI searcher have ILI
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35. Layout
1
System
2
Comparing ILI surveillance systems
3
Epidemic detection
4
Vaccine efficacy
25 October 2013, Rio de Janeiro
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36. ILI baseline
2003 - 2004
2004 - 2005
2005 - 2006
A
ILI / 100,000
1400
2006 - 2007
2007 - 2008
2008 - 2009
2009 - 2010
2010 - 2011
2011 - 2012
2012 - 2013
Baseline
Netherlands
1200
1000
800
600
400
200
0
B
ILI / 100,000
1400
Belgium
1200
1000
800
600
400
200
0
C
ILI / 100,000
1400
Italy
1200
1000
800
600
400
200
0
Sep
Oct
Nov
Dec
Jan
Feb
Mar
Apr
May
Month
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37. Real time monitoring
Influenzanet
95% CI
Baseline
2500
16337 participants (26 Dec)
12409 participants (27 Oct)
ILI / 100,000
2000
1500
1000
500
0
2009
2010
Year
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38. Real time monitoring
Influenzanet
95% CI
Baseline
Model
2500
ILI / 100,000
2000
1500
1000
500
0
2009
2010
Year
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39. Real time monitoring
Influenzanet
95% CI
Baseline
15,000 participants
2500
ILI / 100,000
2000
1500
1000
500
0
2009
2010
Year
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40. Real time monitoring
Influenzanet
95% CI
Baseline
1,000 participants
2500
ILI / 100,000
2000
1500
1000
500
0
2009
2010
Year
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41. Real time monitoring
Influenzanet
2500
95% CI
50000 participants (17 Dec)
10000 participants (8 Nov)
3000 participants (2 Jan)
3000 participants (12 Nov)
1000 participants (11 Jan)
ILI / 100,000
Model
50000 participants (3 Nov)
10000 participants (26 Dec)
2000
Baseline
1000 participants (18 Nov)
1500
1000
500
0
2009
2010
Year
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42. Participation - Totals
Country
Netherlands
Belgium (Flanders)
Portugal
Italy
United Kingdom
Sweden
France
Spain
Pop.
16.8M
6.3M
10.5M
59.4M
63.7M
9.6M
65.6M
46.0M
Participants
13366
3948
1428
1886
5614
2853
5805
592
Active
11642
3609
1147
1164
3616
2310
4559
436
Percentage
0.07%
0.06%
0.01%
0.002%
0.006%
0.02%
0.007%
0.0009%
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43. ILI detection Influenzanet vs. EISN
Influenzanet: ILI / 100,000
Influenzanet
A
Baseline
14 Jan 2009
EISN ILI 2008 - 2009
C
1400
1200
1000
800
600
400
200
0
Nov Dec Jan Feb Mar Apr
D
EISN: ILI / 100,000
27 Dec 2008
95% CI
B
27 Dec 2008
Nov Dec Jan Feb Mar Apr
E
14 Jan 2009
Nov Dec Jan Feb Mar Apr
F
250
200
150
100
50
0
Nov Dec Jan Feb Mar Apr
Nov Dec Jan Feb Mar Apr
Nov Dec Jan Feb Mar Apr
2008 - 2009
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44. ILI detection Influenzanet vs EISN - Table
Season
2003/04
2004/05
2005/06
2006/07
2007/08
2008/09
2009/10
2010/11
2011/12
2012/13
Average
Influenzanet
Wed 10 Dec
Fri 4 Feb
Sat 11 Feb
Sat 17 Feb
Tue 8 Jan
Sat 27 Dec
Thu 29 Oct
Wed 29 Dec
Sun 19 Feb
Fri 28 Dec
EISN
Wed 24
Wed 16
Wed 15
Wed 14
Wed 20
Wed 14
Wed 21
Wed 19
–
Wed 16
Dec
Feb
Feb
Mar
Feb
Jan
Oct
Jan
Jan
Difference
14
12
4
25
43
18
–8
21
–
19
16
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45. Days until GP visit
A
40
B
Sweden
C
UK
D
Netherlands
Belgium
30
Percentage (%)
20
10
0
E
40
<1 1
2
3
4 5-7 >7
Spain
F
<1 1
2
3
4 5-7 >7
France
G
<1 1
2
3
4 5-7 >7
Italy
H
<1 1
2
3
4 5-7 >7
Portugal
30
20
10
0
<1 1
2
3
4 5-7 >7
<1 1
2
3
4 5-7 >7
<1 1
2
3
4 5-7 >7
<1 1
2
3
4 5-7 >7
Days until GP visit
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46. Layout
1
System
2
Comparing ILI surveillance systems
3
Epidemic detection
4
Vaccine efficacy
25 October 2013, Rio de Janeiro
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Influenzanet
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47. Vaccine efficacy
Is Influenzanet an ideal system to monitor vaccine efficacy in real time?
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48. Vaccine efficacy
Is Influenzanet an ideal system to monitor vaccine efficacy in real time?
Influenzanet measures Influenza-like illness (ILI), the vaccine protects
against the influenza virus.
Vaccinated and unvaccinated participants can not be directly
compared (“non-randomized trial”)
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49. Vaccine efficacy: ILI vs Influenza
A
Not vaccinated
Vaccinated
Baseline
1200
ILI / 100,000
1000
800
600
400
200
Viral confirmation
0
B
Influenza A
Influenza B
20
15
10
5
0
Nov
Dec
Jan
Feb
Mar
Apr
May
2008 - 2009
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50. Vaccine efficacy: ILI vs Influenza
Season
A
All ILI onsets
B
Influenza period
C
Inf. period - Baseline
2003 - 2004
2004 - 2005
2005 - 2006
2006 - 2007
2007 - 2008
2008 - 2009
2009 - 2010
2010 - 2011
2011 - 2012
2012 - 2013
0.0 0.4 0.7 1.0 1.3 1.6 2.0
0.0 0.4 0.7 1.0 1.3 1.6 2.0
Risk ratio (vaccine)
0.0 0.4 0.7 1.0 1.3 1.6 2.0
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51. Vaccine efficacy: Risk factors
Most people are vaccinated because they belong to a risk group:
Percentage (%)
Chronic disease
Age over 60
100
80
60
40
20
0
100
Vaccinated beginning season
Not vaccinated
Vaccinated during season
1-17
18-39
40-59
60-99
Reasons for vaccination
GP recommendation
To protect me
To protect others
Part of risk group
Company vaccination
Easily available
Free
Not missing school/work
Always get a vaccine
Other
Percentage (%)
80
60
40
20
0
1-17
Sander van Noort (IGC, Portugal)
18-39
40-59
Influenzanet
60-99
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52. Vaccine efficacy: Risk factors
A
No extra risk factors
VE 2003 - 2004
VE 2004 - 2005
VE 2005 - 2006
VE 2006 - 2007
VE 2007 - 2008
VE 2008 - 2009
VE 2009 - 2010
VE 2010 - 2011
VE 2011 - 2012
VE 2012 - 2013
B
+ Age + Chronic
>= 60
Chronic disease
VE 2003 - 2004
VE 2004 - 2005
VE 2005 - 2006
VE 2006 - 2007
VE 2007 - 2008
VE 2008 - 2009
VE 2009 - 2010
VE 2010 - 2011
VE 2011 - 2012
VE 2012 - 2013
0.0
0.4
0.7
1.0
Risk ratio (vaccine)
1.3
1.6
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53. Other risk factors
Risk factors:
Chronic disease
Children
Parents
Women
Pets
Smoking
No risk:
Using public transport
Living alone (vs with only adults)
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54. Acknowledgments
Netherlands (Carl Koppeschaar, Ronald Smallenburg)
Belgium (Marc van Ranst)
Portugal (Gabriela Gomes, Vitor Faustino)
Italy (Daniela Paolotti)
United Kingdom (John Edmunds)
Sweden (Annasara Carnahan)
France (Vittoria Colizza)
Spain (Yamir Moreno)
Ireland (Jim Duggan)
http://www.influenzanet.eu/results
vanNoort@gmail.com
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