Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove
description
Transcript of Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove
![Page 1: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/1.jpg)
Surveillance, Forecasting, & Nowcasting
in an Influenza Pandemic
Peter G Grove Health Protection Analytical Team
Department of Health
![Page 2: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/2.jpg)
Why Collect Data in a Pandemic?
1) Management of the response to the pandemic.
2) Research to help deal with later pandemics.
3) Public and Ministerial confidence.
![Page 3: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/3.jpg)
Why Collect Data in a Pandemic?
1) Management of the response to the pandemic.
2) Research to help deal with later pandemics.
3) Public and Ministerial confidence.
![Page 4: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/4.jpg)
Advised Planning Assumptions
• Up to 50% of the population ill (with serological rates up to 80-85%).
• Of which, from 10% up to 25% are expected to have complications, half of these bateriological. (With possibly as little a 35% overlap between the ‘at risk groups’ and those who actually get complications.)
• Peak illness rates of 10 - 12% (in new cases per week - of the population) in the peak fortnight.
• Absences rates for illness reach 15-20% in the peak weeks (at a 50% overall attack rate, assuming an average 7 working day absence for those without complications, 10 for those with, and some allowance for those at home caring for children.)
• Case hospitalisation demand rates in the range 0.55% to 4% with an average six day length of stay.
• - but, of which 25% would, if the capacity existed, require intensive care for 10 days.
• Case fatality rates in the range 0.4% to 2.5%.
![Page 5: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/5.jpg)
Scientific Pandemic Influenza Advisory Committee (SPI):
Subgroup on Modelling
www.advisorybodies.doh.gov.uk/spi/minutes
DH website:
![Page 6: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/6.jpg)
Defence in Depth – Because we don’t know if any particular intervention will work, we need packages of interventions.
Pre-pandemic vaccine
Antivirals
AntibioticsSocial
Measures.
Pandemic Specific Vaccine
![Page 7: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/7.jpg)
Main Decisions
• Antiviral Policy
– Current 25% stockpile– Building up to at least 50%– Possibly 75% (or even 125%)
• School Closures
![Page 8: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/8.jpg)
Countermeasures
‘Household Prophylaxis’
0.0%
0.5%
1.0%
1.5%
2.0%
2.5%
0 30 60 90 120 150 180
Days
Da
ily
ca
se
s (
% o
f p
op
) .
No interventions
Treat cases (same day)
Treat+hh prophylaxis
Treat+school closure
Treat+hh proph+schoolclosure
![Page 9: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/9.jpg)
Main Decisions
• Antiviral Policy– Higher raw attack rate.– Reduction in transmission less than expected.– Higher dosing required– Fraud.
• School Closures– If schools were closed, absenteeism due to those staying at
home to look after children could rise to 17-18% throughout the period of school closure, giving a total absence level including illness of 30-35% at the peak
![Page 10: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/10.jpg)
Antiviral Policy
• At 25% level– Treatment of all those ill until effective attack rate is
forecast to exceed 25%– Treatment of Children and at risk groups.
• At 50-75% level– Household Prophylaxis – Treatment of all – Treatment of Children and at risk groups.
![Page 11: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/11.jpg)
Decisions
• If/When to change antiviral strategy?
• Whom to prioritise?
• When to open/close schools?
• (Secondary Antiviral)
![Page 12: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/12.jpg)
Policy Treatment Prophylaxis - run out
Attack rate 30 M 28 M
Peak attack rate 1,100 k/day 740 k/day
Deaths 230 k 350 k
Table: Attack rate and deaths at a 50% raw attack rate
Figure: 50% raw attach rate comparing treatment and prophylaxis until antivirals run out
![Page 13: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/13.jpg)
Severity
• Extreme Pandemic (CFR > ~ 3%)– Close schools– Cancel public events– Household quarantine– Travel restrictions
• Mild Pandemic (CFR < 0.4, AR < 10%)– Revert to usual GP based approach.
![Page 14: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/14.jpg)
Secondary care
• Assistance to localities with specific problems.
![Page 15: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/15.jpg)
From Data to Information -
‘Real Time Modelling’
![Page 16: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/16.jpg)
• None of the decisions can be based on pure data.
• Attack rate estimates depend on long term forecasts.
• ‘Current’ and ‘total’ numbers of cases, deaths and case fatality rates depend on ‘nowcasts’.
![Page 17: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/17.jpg)
Resilience and Alternative Views
• Two approaches• Three teams
– Health Protection Agency Centre for Infections.
– Medical Research Council Centre for Outbreak Analysis
– Health Protection Agency Centre for Emergency Preparedness.
![Page 18: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/18.jpg)
• Daily Nowcasts
• Weekly long term forecasts.
• HPA CfI results official view
• Results compared weekly – discussed with senior officials.
• Implications explained.
![Page 19: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/19.jpg)
Data streams
• Telephone system: – Daily, Current, includes ILI.– Calls.– Antivirals authorised (fraud)– Age– Complications
![Page 20: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/20.jpg)
Databases
• First 100’s of cases
• Clinical database
![Page 21: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/21.jpg)
GPs
• RCGP• QFlu
– Daily. – Complications– Antivirals for children under 3.– Hospitalisations.
![Page 22: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/22.jpg)
• Deaths from National Statistics. – Days or weeks delay.– High level of background.
• Hopitalisations from standard NHS statistics.
![Page 23: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/23.jpg)
FF100
First few 100’s of cases and contacts.
![Page 24: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/24.jpg)
FF100 unique outputs needed for modelling
• Early information on serial interval (and R0 ?)
• Proportion of those infected with clinical symptoms.
– Both need care tracing contacts and viral swabbing/serology.
![Page 25: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/25.jpg)
Other useful outputs
Early information on
– disease course and – severity– initial case numbers for CCC/public.
![Page 26: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/26.jpg)
Winter Willow
Surveillance and Real Time Modelling
![Page 27: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/27.jpg)
• Winter Willow did not exercise real time modelling or surveillance systems directly
• But…
![Page 28: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/28.jpg)
• Large number of simulated data sets, forecasts and reports had to be created.
![Page 29: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/29.jpg)
Simulated data
• Run model to construct epidemic (cases by age, hospitalisations, deaths.)
• Add noise (ILI, delays in reporting)• Create simulated data set.• Run nowcasts and forecasts.• Use reporting system to present to
decision makers.
![Page 30: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/30.jpg)
• Lessons to be learnt from process of creating reports and how they were used.
![Page 31: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/31.jpg)
-
200,000
400,000
600,000
800,000
1,000,000
1,200,000
1,400,000
27
/12
10
/01
24
/01
07
/02
21
/02
07
/03
21
/03
04
/04
18
/04
02
/05
16
/05
da
ily #
ne
w c
linic
al c
as
es
Winter Willow: forecasts at first UK case based on (simulated) WHO information.....
![Page 32: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/32.jpg)
Page 1 of 7
UK Alert level : 4 declared on: 19th February 2006 Report Date: 19th February 2006
Summaryi This week so far Last week total Cumulative total
Estimated Total number of clinical cases ii (modelled data)
220,000 41,000 270,000
Estimated Total number of excess deaths (modelled data)
TBC TBC TBC
Indicative cumulative number of deaths (modelled)
N/A N/A 1272
Total number of antiviral treatment courses distributed
N/A N/A 341,928
Total number of people vaccinated (when available)
N/A N/A NONE
Total number of Trusts with operational difficulties
N/A N/A N/A
Comparison with last report submitted Free text summary: The number of clinical cases is increasingly exponentially in all regions now. The incidence in school-aged children continues to be significantly higher than in other age groups. There continues to be a large discrepancy between the estimated number of cases and the number of antiviral doses given (though the difference is falling). This highlights that many individuals have received antivirals for ILI that was not pandemic influenza in the early phases, but as the incidence increases, the “wastage” rate is now dropping significantly. Although there are many case reports of deaths, the number of deaths reported by ONS is still not above the base-line due to delays between illness onset and death, registration and in reporting of deaths. Graph 1: Cumulative total of clinicalii cases of pandemic influenza broken down by age groupiii
Graph 2: Cumulative total of excess deaths from pandemic influenza broken down by age groupiv
0
20000
40000
60000
80000
100000
120000
140000
27/1
2/20
06
03/0
1/20
07
10/0
1/20
07
17/0
1/20
07
24/0
1/20
07
31/0
1/20
07
07/0
2/20
07
14/0
2/20
07
Est
imat
ed c
um
ula
tive
nu
mb
er o
f ca
ses
<1
1-4
5-14
15-24
25-44
45-64
65+
![Page 33: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/33.jpg)
Table 3. HPA commentary There is considerable uncertainty in projections at present, since the number of reported consultations has only just risen above base-line levels in most regions. In particular, due to the delay between onset and reporting, projections on deaths is speculative, and informed from estimates made from non-UK specific data. Detailed projections on deaths by age and region are therefore not reliable at this time and are therefore not shown. Table 4. Modellers forecasts and projections – Epidemiology (if available) Short-term forecasts (next 5 days): 622,000 new cases are projected to occur in the next 5 days, roughly half of which are expected in children under 15 years age. The table below gives the breakdown of expected cases by region (to nearest 000):
East of England East
Midlands Greater London North East North West South East South West
West Midlands
Yorks & Humber Wales Northern Ireland Scotland
142,000 26,000 215,000 9,000 10,000 151,000 16,000 10,000 10,000 9,000 15,000 9,000 Long-term projections (last updated 19/2/07): The figure compares GP consultation data (red) with model projections (grey). The expected number of cases over the course of the epidemic is 16.1m, with 90% CI from (8-25m). The expected number of excess deaths is 374,000 (90%CI 192,000-593,000). London and the South East are expected to peak in early March, Yorks & Humber, Scotland and North West late March. Other regions are expected to peak around mid-March.
![Page 34: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/34.jpg)
As epidemic develops....
Yorks & Humber
0
5000
10000
15000
20000
25000
30000
35000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
West Midlands
0
5000
10000
15000
20000
25000
30000
35000
40000
45000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
Wales
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
20000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
Greater London
0
10000
20000
30000
40000
50000
60000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
East Midlands
0
5000
10000
15000
20000
25000
30000
35000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
East of England
0
5000
10000
15000
20000
25000
30000
35000
40000
45000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
North East
0
5000
10000
15000
20000
25000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
North West
0
10000
20000
30000
40000
50000
60000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
South East
0
10000
20000
30000
40000
50000
60000
70000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
South West
0
5000
10000
15000
20000
25000
30000
35000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
Scotland
0
5000
10000
15000
20000
25000
30000
35000
40000
45000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
Northern Ireland
0
2000
4000
6000
8000
10000
12000
14000
23-J
an
30-J
an
6-F
eb
13-F
eb
20-F
eb
27-F
eb
6-M
ar
13-M
ar
20-M
ar
27-M
ar
3-A
pr
10-A
pr
17-A
pr
24-A
pr
Rep
ort
ed G
P c
on
sult
atio
ns
![Page 35: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/35.jpg)
• Surveillance and Real-time modelling are critical to management of a pandemic
Lessons
![Page 36: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/36.jpg)
• Windows of opportunity for decision making as modelling evidence builds up.
• Need to set suitable expectations.
• Need to communicate uncertainty.
• Distinction between ‘useful’ modelled outputs and ‘useless’ raw numbers.
![Page 37: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/37.jpg)
Lessons
• Need better process.
• Need better presentation.
![Page 38: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/38.jpg)
National Summary (ranges indicate minimum, median, and maximum estimates)
Previous week(Until [xx-7]-xx-xx)
Last week total(From xx-xx-xx)
Cumulative total since (date)
Nowcast estimate of total number of clinical cases range range range
Nowcast indicative estimate of total number of excess deaths in (based on international experience)
range range range
Nowcast estimate total number of excess deaths in (based on data)
range rangerange
Nowcast estimate of case fatality ratio (based on data) N/A N/A
range
Comparison with last report submittedFree text summary
NOWCAST NATIONAL SUMMARY
Note: Numbers in this section are modelled estimates Both current and past estimates may change from day to day as more information becomes available.
Graph 1: Nowcast cumulative total of clinicalii cases of pandemic influenza broken down by age group[i] Graph 2: Nowcast cumulative total of excess deaths from pandemic influenza broken down by age group[ii] (if modelled data exists)
![Page 39: Surveillance, Forecasting, & Nowcasting in an Influenza Pandemic Peter G Grove](https://reader035.fdocuments.us/reader035/viewer/2022081603/56813f55550346895daa1ba6/html5/thumbnails/39.jpg)
Questions?