Sources of UK flu data: influenza surveillance in the UK
The PHE influenza Surveillance Section, Respiratory Disease Department, coordinates and collates flu surveillance for the UK.
Public Health England’s (PHE’s) Influenza surveillance section at PHE Colindale co-ordinates and collates flu surveillance for the UK.
Influenza is not a notifiable disease. It can cause a wide range of illness from a very mild or asymptomatic infection to a very serious illness which can result in hospitalisation and death.
We use several sources of data to understand influenza activity in the UK. During the influenza season we include data from these sources in the weekly national influenza reports and graphs. Many of the data sources have been used for several years. We developed some new systems during the pandemic in 2009.
Vaccination is the best protection against flu. The World Health Organization (WHO) recommends vaccine composition twice a year, based on reported strains circulating, for the north and south hemispheres.
Clinical surveillance through primary care
Sentinel surveillance schemes based on networks of general practitioners
We gather clinical data from general practitioners’ (GP) surgeries that report the weekly consultations for influenza-like illness (ILI) and other acute respiratory illnesses. These schemes use the number of patients registered with the participating GP as the denominator. In the UK, each country runs their own scheme.
The RCGP weekly returns service, run by the Royal College of General Practitioners since 1966, provide clinical surveillance data and virological specimens from around 100 GP practices across England.
To aid interpretation of the rates and comparison with previous years, we use past years’ data to define for most GP-based schemes to indicate:
- expected rates when influenza is not circulating widely (baseline levels)
- normal seasonal rates of influenza in the winter season
- higher than expected or epidemic activity (see table)
Consultation rates are not directly comparable between schemes.
Those organisations collecting data define flu differently
- RCGP (England) and Health Protection Scotland (HPS) record ‘Influenza-like illness’ (ILI)
- NPHS Wales records ‘influenza’
- PHA (Northern Ireland) records a combined ‘influenza and ILI’ rate
The method of data extraction for each agency differs.
Some schemes only include primary consultations (such as RCGP and NPHS Wales), while HP Scotland records repeat consultations.
We also know the health-seeking behaviour of the populations is different: for example people in Northern Ireland tend to go to the GP more than those in England.
Table: GP-based surveillance schemes for influenza in the UK with links to organisation websites about each scheme.
|Scheme (country)||Baseline||Normal||Above average||Consultation for|
|PHA (Northern Ireland)||70||70-500||>500||ILI/influenza|
The threshold level for Scotland follows the Pandemic Influenza Primary care Reporting (PIPeR) system which currently represents 2% of the Scottish population.
Influenza-like illness (ILI) is the main indicator used for surveillance of respiratory viruses but RCGP weekly returns service also provide rates for other illnesses such as acute bronchitis, which can be an indicator of respiratory syncytial virus (RSV) circulation and pneumonia.
Medical Officers of Schools Association (MOSA) and PHE scheme
Boarding schools in the MOSA scheme send reports of various illnesses, including ILI, to the Respiratory Diseases Department each week during the school terms. Rates are calculated and relayed back to the schools. Up to 42 schools report covering a population of approximately 12,000 pupils. Most of the children are located in the southern half of England, with pupils aged between 5 and 18 years, the majority, however, are boys aged from 13 to 18 years.
Outbreaks of respiratory illnesses
Acute respiratory outbreaks in institutional setting (schools, care homes, hospitals etc.) are reported to the Respiratory Diseases Department at PHE Colindale as they occur. Specialist Microbiology Services Colindale can provide support and advice for the management and investigation of outbreaks. Sampling to identify the virus involved is encouraged.
Community influenza telephone survey
Under the National Institute for Health Research (NIHR) funded Centre for Health Protection Research (CHPR) project ‘Establishing a population-based system for the serological surveillance of influenza in England’, PHE conducted a telephone survey for influenza in approximately 800 households in England during the winter of 2013 to 2014 influenza season to:
- collect data on rates of respiratory illness in the population
- epidemiological information including recent influenza vaccine history, care-seeking behaviour and underlying socio-democratic variables
- recruit potential study participants for a new research study
For this study, ‘Validation of alternative sampling methods for detection of influenza antibodies in a cohort of adults nested in a cross-sectional population telephone survey, study participants provided paired (pre-season and post peak season/convalescent) blood samples collected at their GP’s surgery and oral fluid and dried blood samples (self-collected at home on the same day).
These biological samples will help us develop new assays for influenza antibodies.
This study was reviewed and given a favourable opinion by National Research Ethics Service (NRES) Committee London-Hampstead.
The study was also adopted onto the NIHR Primary Care Research Network portfolio
For further information about the telephone survey, please contact PHE at CIS@phe.gov.uk
Virological analysis by PHE’s Virus Reference Department
The Virus Reference Department (VRD) at PHE provides a reference facility for subtyping and antigenic characterisation of influenza isolates on behalf of PHE and NHS laboratories. VRD analyses about 80% of virus isolates reported in England, Wales, and Scotland.
The genetic and antigenic data derived from this analysis form the basis of data supplied from the UK to the World Health Organization as evidence to guide the annual formulation of the influenza vaccine.
Sentinel virological surveillance schemes
In a normal influenza season, an English GP-based sentinel scheme provides timely information about the proportion of patients presenting to GPs with an influenza-like illness (ILI) who are positive for influenza and the strains of influenza that are circulating in the community:
PHE VRD and RCGP scheme: Throughout the season about 85 general practices in the RCGP scheme in England obtain nose and throat swabs from patients who present with ILI and send these specimens by post to VRD for virus isolation and characterisation.
Real-time PCR for influenza and respiratory syncytial virus (RSV) is carried out on specimens submitted through this scheme.
GP-based sampling schemes also operate in the devolved administrations (DAs) of Scotland, Wales and Northern Ireland.
Routine laboratory reports from hospitals in England and Wales
The Respiratory Disease Department runs a voluntary scheme to collect data on clinical specimens that yield positive results in tests for respiratory pathogens at regional PHE and NHS laboratories. These specimens are mainly taken for diagnostic purposes and almost all laboratories participate in this weekly scheme. The information reported includes
- type of specimen
- method of identification
- age and sex of the patient
Some reports include additional information about cases associated with outbreaks or travel. Laboratories also refer specimens positive for influenza to the VRD for confirmation and further tests.
Data Mart (reports from laboratories in England)
The initial scope of the Data Mart project was to automate the collection of all H1N1 2009 influenza laboratory testing information.
The Data Mart system now incorporates all major respiratory viral test results from the majority of laboratories that took part in the extended PHE ‘Swine Flu testing network’.
The Data Mart system is now serving as an important laboratory surveillance tool for monitoring major respiratory viruses circulating in England. Currently the Data Mart system is using weekly automatic electronic outputs from Barts, Birmingham, Bristol, Cambridge, PHE Colindale, Kings, Leeds, Leicester, Manchester (including Preston), Newcastle, Royal Free, Southampton and UCLH laboratories. A de-duplication process is carried out when new data are uploaded into the system by using patients’ surname, first name initial and date of birth.
Participating labs test for respiratory viruses using real time polymerase chain reaction (RT-PCR) though not all laboratories test for or report all viruses. Tests that Data Mart records include
- human metapneumovirus
- respiratory syncytial virus
As denominator data are available (the total number of patients tested for each virus) we can examine trends in the proportion of samples positive for each virus on a weekly basis.
A sample of influenza-positive specimens are tested for susceptibility to antiviral drugs at VRD. We can fully test a viral isolate to see if it will grow in the presence of an antiviral drug. However this process can take a long time and in some cases it is not possible to grow an isolate from a sample.
In the 2007 to 2008 season a strain of H1 influenza arose which was resistant to oseltamivir (Tamiflu), because of a specific genetic mutation (H275Y).
Testing for this mutation is quicker than the full test, but we cannot class a virus without this mutation as sensitive to the drug, as it may have another resistance-inducing mutation. This same mutation has appeared in the influenza H1N1(2009) virus.
From the 2010 to 2011 season onward regional laboratories in England have the capability to test for antiviral resistance. VRD at Colindale confirms all resistant specimens.
The healthcare associated infections (HCAI) team at PHE Colindale analyse bacterial susceptibility to certain pathogens, known to cause pneumonia as a secondary infection to influenza, using data from regional laboratories. The team monitors trends in age and region over time.
Disease severity and mortality data
Two main systems exist to track illness resulting in hospitalisation:
- A national mandatory collection reports the number of confirmed influenza cases admitted to Intensive Care Units (ICU) and number of confirmed influenza deaths in ICU by trust across the UK. A confirmed case is ‘an individual with a laboratory confirmed influenza infection admitted to ICU’.
Weekly aggregate figures for the number of admissions and deaths are available in the report broken down by flu type or subtype and age group. See UK severe influenza surveillance system: sentinel acute NHS trusts protocol (PDF, 146KB, 5 pages)
- We have recruited NHS Trusts in England to a sentinel scheme to record the weekly number of laboratory confirmed influenza cases hospitalised at all levels of hospital care, also sorted by flu type or subtype, and age group. Where available, we will report further epidemiological data on confirmed cases admitted to ICU and HDU. See UK severe influenza surveillance system: all NHS acute trust protocol (PDF, 170KB, 6 pages)
Deaths due to influenza are difficult to estimate: sometimes deaths are recorded as resulting from pneumonia or another secondary condition. To estimate the effect influenza has on mortality, PHE uses data on weekly all-cause death registrations in England and Wales provided by the Office for National Statistics (ONS).
Using over 20 years of data we have established a baseline of the expected number of deaths registered in each week. A 90% confidence interval allows for uncertainty around these deaths. If the weekly number of registered deaths rises above the top bound of the confidence interval, we count it as an excess of deaths for that week.
As these deaths are due to all causes, we cannot attribute any excess directly to influenza.
EuroMoMo (Mortality Monitoring in Europe) is a project to calculate age-specific and region-specific excess mortality rates across England and Wales.
We track Influenza activity in other countries online:
- World Health Organization (WHO)
- European Centre for Disease Prevention and Control (ECDC)
- other individual countries’ public health authorities.
PHE is also responsible for reporting clinical and virological data on influenza to WHO and ECDC.