Guidance

Sources of surveillance data for influenza, COVID-19 and other respiratory viruses

Updated 8 June 2023

Applies to England

This page summarises the sources of data for the surveillance systems which are used to monitor COVID-19, influenza and other seasonal respiratory viruses in England. COVID-19 is the disease name and SARS-CoV-2 is the virus name.

Much of the data obtained through these surveillance systems is presented in the weekly national influenza and COVID-19 surveillance report.

Laboratory surveillance

Confirmed COVID-19 cases (England)

COVID-19 case reporting in England is monitored using an episode-based definition to include possible reinfections. Each infection episode, beginning with the earliest positive specimen date, is counted separately if there are at least 91 days between positive test results (polymerase chain reaction (PCR) or lateral flow device (LFD)).

In the weekly national influenza and COVID-19 surveillance report, the number and rate of confirmed COVID-19 episodes through Pillar 1 is presented, with Pillar 1 including swab testing carried out in UK Health Security Agency (UKHSA) laboratories and in NHS hospitals (largely covering healthcare workers and those in hospital with clinical need).

From 1 April 2022, the government ended provision of widespread community testing in England, as outlined in the plan for living with COVID-19. Routine asymptomatic testing through NHS settings was paused from 31 August 2022. This, and other changes to testing patterns are important to consider alongside COVID-19 cases, and data should be interpreted in the context of these changes to testing.

Additionally, further changes in testing policy are in effect since 1 April 2023, which may affect case rates and positivity rates. Changes to testing policies over time may affect positivity rates and incidence rates and should be interpreted accordingly.

Further data on COVID-19 cases is available on the coronavirus dashboard.

COVID-19 positivity (England)

COVID-19 positivity reports on the proportion of individuals tested who are positive for SARS-CoV-2. Positivity is presented as positivity by PCR testing only. In reports from week 16 2023 onwards, this is presented as a 7-day rolling average with the number of individuals testing positive during the preceding 7 days divided by the number of individuals tested during the preceding 7 days through PCR testing. As with COVID-19 cases data, positivity data should be interpreted in the context of current testing patterns.

As of July 2021, COVID-19 positivity through PCR testing has been presented in the weekly national influenza and COVID-19 surveillance report.

Respiratory DataMart

The Respiratory DataMart sentinel system was initially set up in 2009 to automate the collection of all influenza A(H1N1)pdm09 laboratory testing information in England. It is now an important sentinel laboratory surveillance tool, monitoring all major respiratory viruses in England, with 17 laboratories contributing data at present through weekly automatic electronic outputs. 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 laboratories test swabs 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 results for include:

  • SARS-CoV-2
  • influenza
  • rhinovirus
  • parainfluenza
  • adenovirus
  • human metapneumovirus
  • respiratory syncytial virus (RSV)

As denominator data is 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. Importantly, this functions as a pseudoprevalence indicator that is relatively stable over time (week to week and year to year) and is less prone to being affected by changes in use of testing that can cause apparent changes in disease prevalence or incidence which can affect indicators that are based on counts or rates.

Most testing reported in Respiratory DataMart is done in patients with a clinical indication for a respiratory virus test. Historically, many SARS-CoV-2 tests have been done as part of admissions screening.

Note that as the Respiratory DataMart system is based on a sample of sentinel laboratories, positivity figures may differ from those obtained through other surveillance systems.

Community surveillance

Acute respiratory infection incidents

Information on acute respiratory infection (ARI) incidents is based on situations reported to UKHSA health protection teams (HPTs) and entered onto the HPZone case and incident management system. These include confirmed outbreaks of acute respiratory infections (2 or more laboratory-confirmed cases of SARS-CoV-2, influenza or other respiratory pathogens) linked to a particular setting, as well as situations where an outbreak is suspected. All suspected outbreaks are further investigated by the HPT in liaison with local partners.

ARI incidents are collated through the public health management system used across all HPTs. Respiratory sampling to identify the virus involved is encouraged.

Several caveats should be considered when interpreting ARI incident data:

  1. The incidents captured on HPZone represent a subset of all ongoing ARI clusters and outbreaks in England rather than an exhaustive listing.

  2. In addition, SARS-CoV-2 testing policies and public health guidance for different settings changed over time. This means that any interpretation of seasonal and temporal trends since March 2020 should take this into account.

  3. It should be noted that the denominator for the different settings will vary significantly. For example, there are fewer hospitals than workplaces. In addition, the propensity to report incidents to UKHSA also varies significantly by setting. This needs to be considered when interpreting the weekly number of reported incidents by setting and caution should be used when making comparisons between settings.

  4. Considering the above, comparisons between regions and settings are not advised as they may be misleading.

  5. From 1 April 2023, changes to COVID-19 testing came into effect, as such data should be interpreted in the context of this change to testing.

Internet-based surveillance

FluSurvey

FluSurvey, started by the London School of Hygiene and Tropical Medicine and now run by UKHSA, provides internet-based surveillance of influenza-like illness (ILI) and COVID-19 symptoms in the UK population. It is part of a European wide initiative (including 11 European countries).

On registration, individuals aged 18 years and over complete a baseline profile questionnaire which collects information on demographic, geographic, socioeconomic (household size and composition, occupation, education, and transportation), and health (vaccination, diet, pregnancy, smoking, and underlying medical conditions) data. Participants can also register to report on household illness.

Subsequently, participants are sent weekly reminders via email to report any symptoms relating to flu or COVID-19 that they may have experienced and their health-seeking behaviour as a result of their symptoms. This creates a fast, reliable and flexible real-time monitoring surveillance system. Participants can also report the number of people they met outside of their household the previous day, to give real-time monitoring of social contact patterns relevant to the spread of infectious diseases.

To register to participate in this scheme or find out more, visit FluSurvey.

Google search queries

This is a web-based syndromic surveillance system that uses daily search query frequency statistics obtained from the Google Health Trends application programming interface (API). This model focuses on search queries about COVID-19 symptoms as well as generic queries about ‘coronavirus’ (for example, ‘COVID-19’). The search query frequency time series has been weighted based on symptom frequency as reported in other data sources. Frequency of searches for symptoms is compared with a baseline calculated from historical daily data.

FluDetector

UKHSA’s predecessor organisation, Public Health England, worked with University College London (UCL) to assess the use of internet-based search queries as a surveillance method for ILI in England. Combining natural language processing and machine learning techniques, a non-linear Gaussian process model was developed by UCL to produce real-time estimates of ILI. This work on early-warning surveillance systems for influenza was developed through the Engineering and Physical Sciences Research Council (EPSRC) Interdisciplinary Research Collaboration (IRC) project i-sense.

The supervised model, trained on historical data from the Royal College of General Practitioners (RCGP) sentinel surveillance scheme (data between 2005 to 2006 to 2016 to 2017 seasons at national level), produces daily ILI estimates based on the proportion of ILI related search queries within a 10% to 15% sample of all queries issued, and is extracted daily from Google’s Health Trends API.

Further information about the FluDetector model is available online.

Syndromic surveillance systems

Syndromic surveillance is the process of collecting, analysing and interpreting health-related data to provide an early warning of human or veterinary public health threats that require public health action.

UKHSA’s real-time syndromic surveillance team (ReSST) coordinates several national syndromic systems by collecting and analysing anonymised health data from several sources, looking for trends indicating higher-than-usual levels of illness and publishing bulletins to keep public health professionals up to date.

Primary care surveillance

Royal College of General Practitioners

The Royal College of General Practitioners (RCGP) Weekly Returns Service, run by the RCGP Research and Surveillance Centre (RCGP RSC) since 1966, provides clinical surveillance data from around 1,900 GP practices across England, with the number of participating practices having grown from around 500 prior to the COVID-19 pandemic. GP consultation rates of ILI, acute bronchitis, pneumonia, lower and upper respiratory tract infections (LRTI and URTI) and COVID-19-like indicators are used to monitor influenza and COVID-19 activity.

UK influenza-like illness consultation rates

Influenza-like illness GP consultation rates are collected in all countries of the UK to monitor influenza activity across countries.

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 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, typically denotes the start of influenza activity or circulation with the breach of subsequent thresholds denoting the intensity of influenza activity in a particular season. The current MEM thresholds are used in the weekly national influenza and COVID-19 surveillance report.

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. It is also important to note that since the COVID-19 pandemic, healthcare-seeking behaviours have changed, affecting patient propensity to consult their GP.

RCGP swabbing

Sentinel swabbing of patients presenting to primary care with ILI is a longstanding surveillance scheme for influenza. The RCGP virology scheme in England includes a subset of participating RCGP practices, with swabbing offered either in-practice or via self-sampling, to patients presenting within 10 days of onset of symptoms of ILI, ARI or COVID-19. The scheme was expanded to include those with COVID-19 symptoms in February 2020 and remains useful for the monitoring of positivity rates of influenza, SARS-CoV-2, RSV and other respiratory viruses in these patients over time.

RCGP serology

Serological surveillance sampling is also undertaking of consenting patients attending for routine blood tests at participating GP surgeries.

Secondary care surveillance

SARI Watch

The Severe Acute Respiratory Infection (SARI-Watch) surveillance system was launched on 5 October 2020. Data is reported from NHS acute trusts in England on the number of laboratory-confirmed influenza, COVID-19 and RSV cases admitted to hospital through a sentinel collection, and the number of intensive care unit (ICU) or high dependency unit (HDU) admissions for laboratory-confirmed influenza and COVID-19 through a mandatory collection.

In previous seasons, surveillance data on hospitalised cases of influenza and RSV as well as Extracorporeal Membrane Oxygenation (ECMO) admissions were collected under the UK Severe Influenza Surveillance System (USISS). COVID-19 hospitalisation data was previously collected under the COVID-19 Hospitalisation in England surveillance system (CHESS). SARI-Watch has replaced both USISS and CHESS.

The weekly rate of new admissions of COVID-19, influenza and RSV cases is based on the trust catchment population of those NHS trusts who made a new return. This may differ from other published figures such as the total number of people currently in hospital with COVID-19.

The MEM method is also applied to SARI-Watch data, allowing the calculation of thresholds which show the impact and intensity of influenza activity in secondary care. The current MEM thresholds are used in the weekly national influenza and COVID-19 surveillance report.

Trends in hospital and critical care admission rates need to be interpreted in the context of testing recommendations. Please note that routine asymptomatic testing for SARS-CoV-2 through NHS settings has been paused from 31 August 2022, therefore SARI-Watch data should be interpreted with this in mind.

Similarly trends in influenza hospitalisation and critical care admission should be interpreted in the context of testing practices. In recent years there has been wider implementation of rapid molecular point of care tests for influenza in hospital settings. From a public health surveillance perspective, it is important to consider a step change in influenza case ascertainment in more recent years.

On 16 February 2023, UKHSA issued a reminder to acute trusts that influenza A samples from critical care should be subtyped in line with existing guidance. This may impact on the ratio of subtyped to unsubtyped in surveillance data.

SARI Watch Severe Respiratory Failure (SRFs) centres

The SARI-Watch surveillance system collects data on every patient admitted to 1 of 6 adult SRF centres in the UK (5 in England and 1 in Scotland). These centres are commissioned by the NHS to provide ECMO, an advanced form of respiratory support for those with acute respiratory failure. All primary causes of admission are captured through SARI-Watch, including admissions for confirmed COVID-19 or influenza infection.

Mortality surveillance

Cumulative COVID-19 deaths

Deaths with COVID-19 by the 28-day definition are reported, which include deaths in individuals with a positive COVID-19 test who died within (equal to or less than) 28 days of the first positive specimen date in the most recent episode of infection. The process for reporting COVID-19 deaths is described online.

Excess all-cause mortality

Seasonal mortality is seen each year in the UK, with a higher number of deaths in winter months compared to the summer. Peaks of mortality above this expected higher level typically occur in winter, most commonly as a result of factors such as cold snaps and increased circulation of respiratory viruses. Influenza has been a particular cause of excess mortality, with COVID-19 being a more significant contributor since 2020. Excess mortality is also often seen in short spells in summer months as a result of heatwaves.

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.

UKHSA monitors and publishes weekly excess all-cause mortality reports, using the EuroMOMO (Mortality Monitoring in Europe) model, which is a European project enabling the comparison of all-cause excess mortality across participating countries in Europe.

A daily model has been developed to monitor excess all-cause mortality during the COVID-19 pandemic. This uses a linear regression model to calculate cumulative excess above baseline (baseline deaths going back 5 years prior to COVID-19), using daily age-group and region-specific all cause deaths as provided daily by the General Register Office (GRO). The deaths were corrected to allow for delay to registration based on past data on these delays. The baseline until November 2020 was from the same day of the year in the previous 5 years plus or minus 7 days with an extrapolated time trend. The baseline from December 2020 to March 2021 only uses the same days plus or minus 7 days from the past 3 low flu years with no trend, and the baseline from April 2021 onwards is set to be the same as the previous years’ baseline.

Microbiological surveillance

Influenza virus characterisation

UKHSA characterises the properties of influenza viruses through one or more tests, including genome sequencing (genetic analysis) and haemagglutination inhibition (HI) assays (antigenic analysis). This data is used to compare how similar the currently circulating influenza viruses are to the strains included in seasonal influenza vaccines, and to monitor for changes in circulating influenza viruses.

The interpretation of genetic and antigenic data sources is complex due to a number of factors, for example, not all viruses can be cultivated in sufficient quantity for antigenic characterisation, so that viruses with sequence information may not be able to be antigenically characterised as well. Occasionally, this can lead to a biased view of the properties of circulating viruses, as the viruses that can be recovered and analysed antigenically may not be fully representative of majority variants, and genetic characterisation data does not always predict the antigenic characterisation.

Influenza antiviral susceptibility

Influenza positive samples are screened for mutations in the virus neuraminidase (NA) and the cap-dependent endonuclease (PA) genes known to confer neuraminidase inhibitor or baloxavir resistance, respectively. The samples tested are routinely obtained for surveillance purposes, but diagnostic testing of patients suspected to be infected with antiviral-resistant virus is also performed.

Antimicrobial susceptibility

Lower respiratory tract isolates of Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, MRSA (Methicillin-resistant Staphylococcus aureus) and MSSA (methicillin-susceptible Staphylococcus aureus) from regional laboratories are tested for antimicrobial susceptibility. These pathogens are important causes of community-acquired pneumonia, often as a secondary infection to influenza. The team also monitors trends in age and region over time.

SARS-CoV-2 variants

UKHSA conducts genomic surveillance of SARS-CoV-2 variants, providing an overview of new and current circulating variants in England, and the prevalence of various UKHSA-designated variants amongst sequenced episodes of SARS-CoV-2 infections. Information on whole genome sequencing coverage is also published. Detailed surveillance of particular variants of concerns can be found in recent technical briefings.

Vaccine uptake

Influenza vaccine uptake

The purpose of the seasonal influenza immunisation programme for England is to offer protection to those who are most at risk of serious illness or death should they become infected with influenza virus.

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.

In 2012, the Joint Committee on Vaccination and Immunisation (JCVI) recommended the phased roll-out of the national influenza vaccination programme to eventually target all children aged 2 to 16 years old (inclusive) in the UK, using the licensed live attenuated influenza vaccine (LAIV). Vaccination of children works directly by protecting the children themselves from influenza infection, and indirectly by reducing influenza transmission to the rest of the population including those at elevated risk of severe consequences of influenza infection.

Influenza vaccine uptake data is collated throughout the vaccination programme, which runs from September to February. Publications on a weekly or monthly basis during this period typically include data on vaccine uptake in:

  • GP patients for those aged 65 and over, those aged 50 to 64 (since December 2020), those in clinical risk groups, children aged 2 and 3, and pregnant women (reported weekly and monthly)
  • frontline healthcare workers (HCWs) working in direct patient care (reported on a monthly basis from September to February)
  • school-aged children, in the cohorts eligible each season (reported on a monthly basis from September to January)

Cohorts eligible for vaccination each winter are set out in the annual flu letter.

Data on vaccine uptake in GP patients is collected through automatic extraction via GP IT system suppliers on a weekly and monthly basis during the influenza season. Data on vaccine uptake in HCWs is collected manually. NHS trusts, GP practices and independent sector healthcare providers submit data via ImmForm, broken down by occupational staff grouping, on the vaccination of frontline HCWs in healthcare-providing organisations from which they commission services. Data on uptake in school age children is collected manually from local authorities.

More information on Influenza vaccine uptake guidance and the latest coverage data is available online.

COVID-19 vaccine uptake

Administration of COVID-19 vaccinations began in England on 8 December 2020. Vaccine coverage and uptake in eligible groups is published weekly, to monitor the roll-out of the COVID-19 vaccination programme.

Cumulative data on vaccine uptake in the general population of England is extracted from the National Immunisation Management Service (NIMS), and published in the weekly national influenza and COVID-19 surveillance report.

Data on COVID-19 vaccine in frontline HCWs is published separately in the COVID-19 vaccine uptake in frontline healthcare workers monthly reports. For comparable COVID-19 and influenza vaccine uptake, please see the Seasonal flu and COVID-19 vaccine uptake in frontline healthcare workers monthly data reports.

International situation

The international situation of influenza and COVID-19 is monitored through several online sources. These include international and regional World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) reports and other countries’ national surveillance data. We also monitor recent information on avian influenza and MERS-CoV through WHO reports and disease outbreak news.