The influenza surveillance section of PHE's Respiratory Disease Department coordinates and collates flu surveillance for the UK.
Public Health England’s (PHE’s) influenza surveillance section in Colindale co-ordinates and collates flu surveillance for the UK.
Influenza is not a notifiable disease. It can cause a wide range of illnesses, 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 Royal College of General Practitioners (RCGP) weekly returns service, run by the RCGP since 1966, provides clinical surveillance data from around 360 GP practices across England and virological specimens from approximately 100 of these.
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.
To aid interpretation of the rates and comparison with previous years, the UK has adopted a standardised method of reporting influenza activity, the Moving Epidemic Method (MEM), used by the European Centre for Disease Prevention and Control.
The MEM method uses historical data (using the previous 10 seasons’ data) to evaluate the timing and duration of an influenza epidemic through a series of cut points, baseline, low, medium, high and very high thresholds. The initial baseline threshold, once breached, denotes the start of influenza activity or circulation with the breach of subsequent thresholds denoting the intensity of influenza activity in a particular season.
This method allows for comparability between the countries of the UK and with other European countries as we know there are differences in the sensitivity of these reporting systems due for example to differences in patient consulting behaviour.
Table 1: Represents the overall (all ages) MEM thresholds for GP sentinel systems for the 2019 to 2020 season by UK countries with links to each organisation’s website.
|12.7 to <24.1
|24.1 to <70.6
|11.1 to <19.4
|19.4 to <57.1
|57.1 to <91.9
|26.7 to <37.2
|37.2 to <154.4
|154.4 to <289.7
|PHA (Northern Ireland)
|14.7 to <23.9
|23.9 to <73.9
|73.9 to <121.7
Medical Officers of Schools Association (MOSA) and PHE scheme
Boarding schools in the MOSA scheme send reports of various illnesses, including ILI, to the Influenza Surveillance section each week during the school terms. Rates are calculated and relayed back to the schools. Around 20 schools reported last season (2018 to 2019), covering a population of approximately 15,000 pupils. For further information about the scheme or if you are a MOSA school and would like to participate in the scheme, email email@example.com
Outbreaks of respiratory illnesses
Acute respiratory outbreaks in an institutional setting, like schools, care homes, and hospitals, are reported to the Influenza Surveillance section at PHE Colindale as they occur using the reporting form below. Specialist Microbiology Services Colindale can provide support and advice for the management and investigation of outbreaks. Respiratory sampling to identify the virus involved is encouraged.
Flusurvey is part of a European wide initiative (including 10 European countries). FluSurvey is run by Public Health England, to monitor influenza-like illness (ILI) activity in the UK population, through an internet-based surveillance system.
On registration, individuals complete a baseline questionnaire which includes demographic, geographic, socio-economic (household size and composition, occupation, education, and transportation), and health (influenza,vaccination, diet, pregnancy, smoking, and underlying medical conditions) data. Subsequently, participants were sent weekly reminders to report any symptoms relating to flu that they may have experienced and their behaviour as a result of their symptoms (health-seeking behaviour).
To register to participate in this scheme or find out more please visit Flusurvey.
PHE and University College London (UCL) have collaborated to assess the use of internet-based search queries as a surveillance method for ILI, throughout England.
This is part of work on early-warning surveillance systems for influenza, through the Engineering and Physical Sciences Research Council – Interdisciplinary Research Collaborations (EPSRC IRC) project i-sense.
The FluDetector model (https://fludetector.cs.ucl.ac.uk/) is a supervised, non-linear Gaussian process model trained on historical Royal College of General Practitioners (RCGP) ILI data. Daily ILI estimated rates are produced based on the proportion of ILI related search queries within a 10%-15% sample of all queries issued, extracted daily from Google’s Health Trends Application Programming Interface (API).
For the 2019 to 2020 season, the baseline MEM threshold (using the previous 10 seasons’ data) for the FluDetector model is 11.9 per 100,000.
Virological analysis by PHE’s Virus Reference Department
The Respiratory Virus Unit (RVU) at PHE provides a reference facility for subtyping and antigenic characterisation of influenza isolates on behalf of PHE and NHS laboratories. RVU 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 England, there are 2 sentinel GP swabbing schemes, which run throughout a normal influenza season, providing 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 RVU and RCGP scheme: throughout the season about 100 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 RVU for virus isolation and characterisation
PHE Specialist Microbiology Network (SMN) scheme: PHE laboratories and the influenza surveillance team recruit GPs to the scheme each season and request GPs to obtain swabs from patients who present with ILI and fill out a patient questionnaire - the samples are sent to the GPs’ local laboratory and results are collated by the national influenza surveillance team at PHE
Real-time PCR for influenza and respiratory syncytial virus (RSV) is carried out on specimens submitted through both schemes.
GP-based sampling sentinel surveillance schemes also operate in the devolved administrations (DAs) of Scotland, Wales and Northern Ireland.
Respiratory DataMart (reports from laboratories in England)
The initial scope of the Respiratory DataMart project in 2009 was to automate the collection of all influenza A(H1N1)pdm09 laboratory testing information in England.
The Respiratory DataMart system now incorporates all major respiratory viral test results from the majority of laboratories that took part in the extended PHE pandemic flu testing network.
The Respiratory DataMart system now serves as an important laboratory surveillance tool for monitoring major respiratory viruses circulating in England. Currently the DataMart system is using weekly automatic electronic outputs from Birmingham, Bristol, Cambridge, PHE RVU (Colindale), Kings, Leeds, Leicester, Manchester (including Preston), Newcastle, Nottingham, Royal Free Hospital, Southampton and Truro laboratories. A de-duplication process is carried out when new data is uploaded into the system by using the patient’s surname, first name initial, date of birth and 6-week episode period.
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 DataMart 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.
The MEM method has been applied to calculate thresholds for the proportion of samples positive for influenza through the Respiratory DataMart scheme since 2013 to 2014.
For the 2019 to 2020 season, the overall (all ages) baseline MEM threshold (using the previous 9 seasons’ data) for the Respiratory DataMart scheme is 9.7%.
A sample of influenza-positive specimens are tested for susceptibility to antiviral drugs at RVU. 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)pdm09 virus.
Since the 2010 to 2011 season, regional laboratories in England have been able to test for antiviral resistance. RVU at Colindale confirms all resistant specimens.
The healthcare associated infections (HCAI) team at PHE Colindale analyse antibiotic susceptibility for certain bacterial 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
UK Severe Influenza Surveillance Schemes (USISS)
The USISS scheme is divided into 2 systems to track illness resulting in admission to secondary care:
- USISS mandatory scheme: a national mandatory collection (USISS mandatory ICU scheme) is operating in co-operation with the Department of Health and Social Care and NHS Digital to report the number of confirmed influenza cases admitted to intensive care units (ICU) and high dependency units (HDU) and number of confirmed influenza deaths in ICU/HDU across the UK - a confirmed case is defined as an individual with a laboratory confirmed influenza infection admitted to ICU/HDU
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.
- USISS sentinel scheme: 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 sub type, and age group - where available, we will report further epidemiological data on children aged 16-years and under admitted to hospital with confirmed influenza
The MEM method has been applied to calculate thresholds to show the impact/intensity of influenza activity through both USISS schemes since 2017 to 2018
Table 2: Represents the overall (all ages) MEM thresholds (using the previous 5 seasons’ data) for the USISS schemes for the 2019 to 2020 season.
|Mandatory (ICU/HDU rate per 100,000)
|0.10 to <0.27
|0.27 to <0.63
|0.63 to <0.91
|Sentinel (Hopitalisation rate per 100,000)
|0.99 to <2.65
|2.65 to <7.87
|7.87 to <12.73
Seasonal mortality is seen each year in the UK, with a higher number of deaths in winter months compared to the summer. Additionally, peaks of mortality above this expected higher level typically occur in winter, most commonly the result of factors such as cold snaps and increased circulation of respiratory viruses, in particular influenza.
Weekly mortality surveillance presented here aims to detect and report acute significant weekly excess mortality above normal seasonal levels in a timely fashion.
Excess mortality is defined as a significant number of deaths reported over that expected for a given point in the year, allowing for weekly variation in the number of deaths. The aim is not to assess general mortality trends or precisely estimate the excess attributable to different factors, although some end-of-winter estimates and more in-depth analyses (by age, geography etc.) are undertaken.
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.
Vaccination uptake and coverage
Influenza vaccine uptake data is collated by the Influenza Surveillance section at PHE Colindale. The vaccine uptake data includes:
- GP patients for those aged 65 and over; those in clinical risk groups; 2 and 3 year olds; and pregnant women (reported on a weekly and monthly basis)
- Frontline healthcare workers (reported on a monthly basis October to February)
- Childhood programme for those of primary school age (reported on a monthly basis throughout the influenza season).
The purpose of the traditional seasonal influenza immunisation programme for England is to offer protection to those who are most at risk of serious illness or death should they develop influenza. In 2012, the Joint Committee on Vaccination and Immunisation (JCVI) recommended the roll-out of a universal childhood influenza vaccine programme with a newly licensed live attenuated influenza vaccine (LAIV).
Ultimately this programme will target all children 2 to 17 years of age with the aim to both directly protect the vaccinated children themselves and by reducing influenza transmission, indirectly protect the rest of the population including those at elevated risk of the severe consequences of influenza infection. In addition to this, frontline health care workers involved in direct patient care are encouraged to receive a seasonal influenza vaccination annually to protect themselves and their patients from influenza.