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

• Initial Cases– Containment phase up to 5th July

• Surveillance in Scotland– GP Consultation Rates– NHS24 telephone– Mortality– AntiViral Prescriptions

Epidemic Curve during Containment Phases

Date of symptom onset

Count of Cases

temporary change in the implementation of the containment policy led to a cessation of universal swabbing in South Glasgow (the then “hotspot” for transmission)

Schools closing

Geographical location of initial cases

Geographical location of initial cases

Deprivation

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

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

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.

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

Location of PTI Practices

PiperGpassEMISVision

• 37 of the 58 practices– All 37 run GPASS

• 211542 Patients – 4% Scottish

Population– Not a total

geographic coverage

020

4060

8010

012

014

0All Patients

ILIARI excluding Asthma - PIPER LEVEL 4

2003-10-01 to 2009-09-07

Dai

ly C

onsu

ltatio

n R

ate

per 1

0000

0

2004 2005 2006 2007 2008 2009

020

4060

8010

012

0

2008-10-01 to 2009-10-26

Dai

ly C

onsu

ltatio

n R

ate

per 1

0000

0

2009 2010

Data2008/09 Trend99% Confidence Limits

2007/08 Trend

Consultation Rates PIPeR Practices

Model

i

iiii mwds log

iiii yVarODPy ),(~

idsiw

Expected Count on Day iSpline trend for Day (time) knots every week

= 1 of Day i is a weekend or holiday,

=0 otherwise

Observed Count on Day i

ih = 1 of Day i is a Monday,

=0 otherwise

Library mgcv in R

050

100

150

2008-10-01 to 2009-10-26

Dai

ly C

onsu

ltatio

n R

ate

per 1

0000

0

2009 2010

Data2008/09 Trend99% Confidence Limits

2007/08 Trend

Consultation Rates PIPeR Practices Age 5-14

020

4060

80

2008-10-01 to 2009-10-26

Dai

ly C

onsu

ltatio

n R

ate

per 1

0000

0

2009 2010

Data2008/09 Trend99% Confidence Limits

2007/08 Trend

Consultation Rates PIPeR Practices Age 15-64

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

Modeli iii wd log

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j j

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32

32

21

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jjj

jjj

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yr

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

id

iw

Expected Count on Day iDay

= 1 of Day I is a weekend

or holiday, =0 otherwiseObserved Count on Day i

2,1max jj r

Date, beginning in 2008

Cou

nt

01/10 30/11 29/01 30/03 29/05 28/07 26/09

050

010

0015

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ObsExpUL

Scotland.CR ColdsFlu99% Exceedance - Created 2009-10-28

28 Days Centred - Linear

Mortality

• Daily Extract of all registered deaths in Scotland supplied by GRO Scotland

• Age, • Gender, • Partial Postcode• Date of Death and,• Date of Registration

Models

i

ias

iasasias

dsd

log

)(~ ii Poissony

idsiw

Expected Count on Day iSpline trend for Day (time) knots every week

= 1 of Day i is a holiday,

=0 otherwise

Observed Count on Day i

im factor denoting separate working days Monday to Friday

Library mgcv in R

iasiasi

iasasi

mhdsd

log

Date of Death Date of Registration of Death

i – Indexes daysa – Age Groups - Gender

Date of Death (2008-10-01 to 2009-10-27)

Dea

ths

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov

120

140

160

180

200

220

All DeathsSmoothed Previous Years + 99% Prediction Interval

DataFitted TrendPredicted Range

Under ReportingCorrection

Date of Registration of Death (2008-10-01 to 2009-10-27)

Dea

ths

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov

010

020

030

040

050

060

070

0

All DeathsSmoothed Previous Years + 99% Prediction Interval

DataFitted TrendPredicted Range

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

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Ayrshire & Arran

Date

Rat

e pe

r 100

000

17/08 10/09 05/100

5010

015

0

Borders

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Dumfries & Galloway

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Fife

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Forth Valley

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Greater Glasgow & Clyde

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Grampian

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Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Highland

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Rat

e pe

r 100

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17/08 10/09 05/10

050

100

150

Lanarkshire

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Rat

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r 100

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17/08 10/09 05/10

050

100

150

Lothian

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Orkney

Date

Rat

e pe

r 100

000

20/08 14/09 08/10

050

100

150

Shetland

Date

Rat

e pe

r 100

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17/08 10/09 05/10

050

100

150

Tayside

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e pe

r 100

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100

150

Western Isles

Date

Rat

e pe

r 100

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150

250

Scotland

Raw unadjusted consultation rates

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

Model

ijk

kkkkkijijk

ijk HBPTISystemPTISystemP

:log

ijkijkijkijk yVarODPy ),(~

Expected Count in Practice k, for age group i and gender j

Observed Count on a Day

ijkP Population in Practice k, for age group i and gender j

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

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Ayrshire & Arran

Date

Rat

e pe

r 100

000

17/08 10/09 05/100

5015

025

0

Borders

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Dumfries & Galloway

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Fife

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Forth Valley

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Greater Glasgow & Clyde

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Grampian

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Highland

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Lanarkshire

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Lothian

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Orkney

Date

Rat

e pe

r 100

000

20/08 14/09 08/10

050

150

250

Shetland

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Tayside

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

150

250

Western Isles

Date

Rat

e pe

r 100

000

17/08 10/09 05/10

050

100

150

Scotland

Adjusted consultation rates

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

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

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

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?