H1N1 in Scotland: Epidemiology and Surveillance

1. H1N1 in Scotland:Epidemiology and Surveillance Chris Robertson, Kim Kavanagh, Adam Wagner Jim McMenamin, Heather Murdoch, Arlene Reynolds, Eisin Shakir, Martin Donaghy Strathclyde University Health Protection Scotland

2. Initial Cases • Containment phase up to 5th July • Surveillance in Scotland • GP Consultation Rates • NHS24 telephone • Mortality • AntiViral Prescriptions

3. Epidemic Curve during Containment Phases Count of Cases Schools closing Date of symptom onset temporary change in the implementation of the containment policy led to a cessation of universal swabbing in South Glasgow (the then “hotspot” for transmission)

4. Geographical location of initial cases

5. Geographical location of initial cases

6. Deprivation

7. Summary • Initial outbreak • Predominantly located in Glasgow area • But evidence of spread throughout central Scotland • Mainly those aged 0-25 affected • But not heavily weighted among school age children • Mainly those in high deprivation groups affected • Serial interval median of 3 days, range 0-10 • R0 – average number of new infections • 1.31 (95% CI 1.30-1.32) Exponential Method • 1.25 (95% CI 1.23 – 1.27) Wallinga Teunis (AJE, 2006) Colleagues at Health Protection Agency, Colindale: Ben Cooper, Marc Baguelin, Stefan Flasche, Nick Andrews

8. Surveillance • GP Consultation Rates • Sample of nasal swabs from patients presenting at GPs with acute respiratory symptoms • NHS24 telephone • Mortality • AntiViral Prescriptions • Hospitalisations Weekly HPS Situation Report Influenza A H1N1v http://www.hps.scot.nhs.uk/resp/swineinfluenza.aspx

9. General Practitioners • There are 1031 Scottish GP practices • 14 Health Boards • 3 very small (Western Isles, Orkney, Shetland) • 1 has over 25% of population (Greater Glasgow and Clyde) • Four main software systems for recording their patient consultation information.  • GPASS (67% of practices) • EMIS (8%) • INPS (Vision) (24%) • Ascribe (1%) • Furthermore, 58 practices within Scotland are part of the PTI network.

10. Pandemic Influenza Primary care Reporting (PIPeR) This system has been designed from the outset to meet the surveillance needs in the event of a pandemic of influenza developing. The scheme is drawn from GP practices which participate in the Practice Team Information (PTI) scheme (formerly the Continuous Morbidity Recording – CMR – team) coordinated by NSS ISD. This is a network of GP’s who receive an annual financial incentive to record all of their practice data electronically. The clinical component presents both ILI and Acute Respiratory Infections (ARI) in recognition of the previous finding that many individuals (particularly children) have their influenza recorded under an ARI rather than an ILI category. All ILI and ARI Read Codes are extracted daily

11. 37 of the 58 practices • All 37 run GPASS • 211542 Patients • 4% Scottish Population • Not a total geographic coverage

14. Model Expected Count on Day i Spline trend for Day (time) knots every week = 1 of Day i is a weekend or holiday, =0 otherwise = 1 of Day i is a Monday, =0 otherwise Observed Count on Day i Library mgcv in R

17. NHS24 • Confidential health advice and information service for people in Scotland • NHS 24 works in partnership with local NHS Boards out-of-hours services to provide patients with health advice and help when GP practices are closed. • About 25,000 – 40,000 total calls per week • Surveillance system running since Jan 2004 monitoring 12 syndromes in 14 health boards

18. Model Expected Count on Day i Day = 1 of Day I is a weekend or holiday, =0 otherwise Observed Count on Day i Farrington CP, et al. A Statistical Algorithm for Early Detection of Outbreaks of Infectious Disease. Journal of the Royal Statistical Society Series A 1996; 159:547-563

20. Mortality • Daily Extract of all registered deaths in Scotland supplied by GRO Scotland • Age, • Gender, • Partial Postcode • Date of Death and, • Date of Registration

21. Models Date of Death Date of Registration of Death Expected Count on Day i Spline trend for Day (time) knots every week = 1 of Day i is a holiday, =0 otherwise i – Indexes days a – Age Group s - Gender factor denoting separate working days Monday to Friday Observed Count on Day i Library mgcv in R

25. Scottish GP Surveillance System • Expansion of the GP Surveillance system to cover daily consultations by 1031 GPs in Scotland • GPASS (67% of practices) • EMIS (8%) • INPS (Vision) (24%) • Ascribe (1%) • 58 practices in PTI network • A similar system worked well last year for winter flu vaccine uptake • Currently 89% of practices participating

26. Raw unadjusted consultation rates

27. Issues • 4 GP recording systems • Systematic differences between then • 58 PTI practices • enhanced training for recording consultations • Health Boards cannot be compared as each health board predominantly used one system • E.g.Greater Glasgow and Clyde GPASS

28. Model Expected Count in Practice k, for age group i and gender j Population in Practice k, for age group i and gender j Observed Count on a Day

29. Modelling • Trying to get a reasonably robust model • which captures the essential features and • which can then be used to adjust the data to provide an ‘all Scotland’ picture • within hours of receiving the completed data

30. Adjusted consultation rates

31. Statistical Issues • Relatively large amount of daily data • Summarised and modelled for reporting that day • Models need to take into account • Known biases in data collection • Systematic trend • Reporting delays • Holidays • Mostly automatic and it is difficult to foresee all the data checks that are required

32. Statistical Issues • Reporting is all based upon modelling using historic data to predict expected patterns this year • Flexible models using splines for the trend plus parameters for known systematic effects • Systems are brought in very quickly with limited time for testing and investigation • Need to be very aware of data quality and the mechanisms for data capture to interpret the data correctly • Need to be open about the models and method of analysis used

33. Position in Scotland • Daily consultation rates (age/gender) • Daily NHS call data (age) • Daily Hospitalisations (Individual records) • Daily deaths (age/gender) • Daily antiviral prescriptions • All electronic data capture and reporting • Weekly Laboratory testing of a planned 500 swabs from symptomatic patients per week (80 - 100 achieved over summer) • Using excellent data capture systems to increase the size of the surveillance to provide local level information

34. Position in Scotland • Great effort by a large number of people in government and health service organisations, laboratories and registrars offices to provide valuable data on a daily basis • Individual and GP level data which is anonymised but can be linked. • Will systems be robust in the event of a huge increase in the number of cases?