Virology surveillance
Episodes of influenza, RSV and COVID-19
The number of influenza episodes remained stable in week 40, with 60 reported, compared to 58 in week 39.
RSV episodes increased from zero in week 39 to seven in week 40. COVID-19 episodes remained stable, with 86 reported in week 40 compared with 88 in week 39 (Figure 2.1).
Episode rates by age group for influenza, RSV and COVID-19 are shown in Figure 2.2. In week 40, the highest influenza and RSV episode rates were recorded in the 0-4 age group (14.4 and 5.8 per 100,000 population, respectively), while the highest COVID-19 episode rate was observed in the 75+ year age group (22.1 per 100,000 population).
Episode rates across local government districts (LGD) for influenza, RSV and COVID-19 are shown in Figure 2.3. In week 40, the highest influenza episode rate was recorded in Lisburn and Castlereagh (5.9 per 100,000 population), the highest RSV rate in Derry City and Strabane (1.3 per 100,000 population), and the highest COVID-19 rate in Newry, Mourne and Down (7.1 per 100,000 population).
Supplementary tables of unique episodes and weekly episode rates are provided at the end of this report.
Testing and positivity (%)
In week 40, there were 1,698 influenza tests, 1,161 RSV tests and 1,798 COVID-19 tests. Positivity was 3.6% (61 positive tests) for influenza, 0.6% (seven positive tests) for RSV and 5.5% (99 positive tests) for COVID-19. Compared to week 39, influenza, RSV and COVID-19 positivity remained stable at 3.5%, 0.0% and 5.7%, respectively (Figure 2.4).
Age-specific positivity rates for influenza, RSV and COVID-19 are shown in Figure 2.5. In week 40, the highest influenza positivity was observed in the 5-14 age group (7.9%), the highest RSV positivity in the 0-4 age group (3.9%), and the highest COVID-19 positivity in the 75+ age group (7.8%).
Supplementary tables of testing and positivity are provided at the end of this report.
Shading represents 95% confidence intervals.
Shading represents 95% confidence intervals.
In week 40, rhinovirus had the highest positivity (18.6%; based on 505 tests performed). Positivity was lower for adenovirus (2.2%), parainfluenza (1.4%) and human metapneumovirus (hMPV) (0.6%), based on 509 tests performed for each pathogen. Compared with week 39, positivity decreased for rhinovirus and parainfluenza, while adenovirus and hMPV positivity remained low and relatively stable (Figure 2.6).
Shading represents 95% confidence intervals.
Influenza sub-typing
Of the 60 new influenza episodes identified in week 40, 54 were influenza A, including 14 influenza A(H1), five influenza A(H3) and 35 influenza A (not subtyped). The remaining six episodes were influenza B (Figure 2.7).
A supplementary table of influenza sub-typing is shown at the end of this report.
Sentinel surveillance
Sentinel surveillance contributes to monitoring and understanding the spread and impact of respiratory viruses, including influenza, RSV and COVID-19, in the community. It involves the systematic collection of data from a geographically representative network of GP practices, covering approximately 17.6% of the Northern Ireland GP registered population, to provide insights into virus activity across Northern Ireland.
In week 40, four of 37 samples submitted to the Regional Virus Laboratory (RVL) were positive for influenza (10.8% positivity), including three influenza A (H1) and one influenza A (H3). No samples tested positive for RSV. Two of 37 samples were positive for COVID-19 (5.4% positivity) (Table 1).
Sentinel detections of influenza, RSV and COVID-19 by age group during the previous year are shown in Figures 2.8, 2.9 and 2.10. Cumulative detections for the 2026/27 influenza season are shown in Table 2.
A supplementary table of testing and positivity is provided at the end of this report.
Table 1. Total sentinel tests and positivity for Influenza, RSV and COVID-19, current week |
|---|
|
| Total Tests | Total Positives | Positivity (%) |
|---|
2026 - 40 | Influenza | 37 | 4 | 10.8 |
2026 - 40 | RSV | 38 | 0 | 0.0 |
2026 - 40 | COVID-19 | 37 | 2 | 5.4 |
Table 2. Total sentinel cases of Influenza, RSV and COVID-19 by age group, Week 40 - current week, 2026/27 |
|---|
| 0-4 | 5-14 | 15-44 | 45-64 | 65-74 | 75+ | Total |
|---|
Flu A (H1) | 0 | 2 | 0 | 0 | 1 | 0 | 3 |
Flu A (H3) | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
Flu A (not subtyped) | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Flu B | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
RSV | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
COVID-19 | 0 | 0 | 0 | 1 | 1 | 0 | 2 |
Non-sentinel surveillance
Non-sentinel surveillance monitors respiratory viruses using virology data collected from healthcare settings, including hospitals and non-sentinel GP practices. This provides information on virus activity across Northern Ireland.
In week 40, 57 of 1,661 samples submitted across laboratories in Northern Ireland were positive for influenza (3.4% positivity), including 12 influenza A (H1), four influenza A (H3), 35 influenza (not subtyped), and six influenza B. RSV was detected in seven samples (0.6% positivity), while 97 of 1,761 samples tested positive for COVID-19 (5.5% positivity) (Table 3).
Non-sentinel detections of influenza, RSV and COVID-19 by age group during the previous year are shown in Figures 2.11, 2.12 and 2.13. Cumulative detections for the 2026/27 influenza season are shown in Table 4.
A supplementary table of testing and positivity is provided at the end of this report.
Table 3. Total non-sentinel tests and positivity for Influenza, RSV and COVID-19, current week |
|---|
|
| Total Tests | Total Positives | Positivity (%) |
|---|
2026 - 40 | Influenza | 1,661 | 57 | 3.4 |
2026 - 40 | RSV | 1,123 | 7 | 0.6 |
2026 - 40 | COVID-19 | 1,761 | 97 | 5.5 |
Table 4. Total non-sentinel cases of Influenza, RSV and COVID-19 by age group, Week 40 - current week, 2026/27 |
|---|
| 0-4 | 5-14 | 15-44 | 45-64 | 65-74 | 75+ | Total |
|---|
Flu A (H1) | 1 | 0 | 1 | 4 | 2 | 4 | 12 |
Flu A (H3) | 3 | 0 | 0 | 0 | 0 | 1 | 4 |
Flu A (not subtyped) | 9 | 6 | 4 | 4 | 5 | 7 | 35 |
Flu B | 2 | 1 | 3 | 0 | 0 | 0 | 6 |
RSV | 6 | 0 | 1 | 0 | 0 | 0 | 7 |
COVID-19 | 11 | 0 | 11 | 14 | 14 | 47 | 97 |
SARS-CoV-2 variants
In the 8 weeks 03 August 2026 to 27 September 2026, 125 COVID-19 samples were sequenced. Of these, 53 were XFG (42.4% of all sequenced samples), 25 were LP.8.1 (20.0% of all sequenced samples), 22 were JN.1 (17.6% of all sequenced samples), 9 were NB.1.8.1 (7.2% of all sequenced samples) and 4 were XFG.3 (3.2% of all sequenced samples). Due to small numbers of samples sequenced, the level of confidence in precision of the estimate is low, and the percentages of each variant may change as further results become available. A more detailed COVID-19 Genomics Bulletin containing a further breakdown of sub-lineages is published weekly.
Parent lineages displayed are subject to change based on lineages under monitoring by the UKHSA horizon scanning team.
Recombinant refers to any recombinant lineage, starting “X”, that does not fall under the parent lineage of a defined variant.
Primary care surveillance
Consultation rates for influenza/influenza-like-illness (‘flu/ILI’)
The general practice (GP) flu/ILI consultation rate during week 40 was 6.6 per 100,000 population, an increase from 5.4 per 100,000 population in week 39. Activity is at low levels (6.5 to <24.1 per 100,000 population) (Figure 3.1).
GP flu/ILI consultation rates by age group and Health and Social Care Trust (HSCT) are shown in Figures 3.2 and 3.3, respectively. In week 40, the highest consultation rate was observed in the 0-4 age group (10.1 per 100,000 population) and in the Western Trust (14.6 per 100,000 population).
Supplementary tables of GP consultation rates are provided at the end of this report.
The baseline MEM threshold for Northern Ireland is <6.5 per 100,000 population for 2026/27. Low activity is 6.5 to <24.1, moderate activity 24.1 to <43.6, high activity 43.6 to <56.8 and very high activity is >56.8 per 100,000 population.
Consultation rates for acute respiratory infection (ARI)
The GP acute respiratory infection (ARI) consultation rate during week 40 was 199.5 per 100,000 population, an increase from 195.1 per 100,000 population in week 39 (Figure 3.4).
GP ARI consultation rates by age group and HSCT are shown in Figures 3.5 and 3.6, respectively. In week 40, the highest consultation rate was observed in the 0-4 age group (738.3 per 100,000 population) and in the Western Trust (311.0 per 100,000 population).
Supplementary tables of GP consultation rates are provided at the end of this report.
Consultation rates for COVID-19
The GP COVID-19 consultation rate during week 40 was 1.0 per 100,000 population, similar to week 39 (1.2 per 100,000 population) (Figure 3.7).
GP COVID-19 consultation rates by age group and HSCT are shown in Figures 3.8 and 3.9, respectively. In week 40, the highest consultation rate was observed in the 75+ age group (2.3 per 100,000 population) and in the Belfast Trust (2.0 per 100,000 population).
Supplementary tables of GP consultation rates are provided at the end of this report.
Secondary care surveillance
Admissions and occupancy
There were 60 new community-acquired emergency hospital admissions during week 40, compared with 46 in week 39 (Figure 5.1). Of the admissions reported in week 40, 21 were influenza A, three were influenza B, three were RSV and 33 were COVID-19. In week 39, 18 were influenza A, two were influenza B and 26 were COVID-19.
Community-acquired emergency hospital admission rates by age group are shown in Figure 5.2. In week 40, the highest admission rate for influenza was observed in the 0-4 age group (4.8 per 100,000 population), the highest RSV rate was also observed in the 0-4 age group (2.9 per 100,000 population), and the highest COVID-19 rate was observed in the 75+ age group (9.6 per 100,000 population).
Supplementary tables of emergency hospital admissions and age-specific admission rates are provided at the end of this report.
By week 40, there had been 24 cumulative community-acquired emergency influenza admissions, three RSV admissions and 33 COVID-19 admissions (Figures 5.3, 5.4 and 5.5. At the same point in the previous season, cumulative admissions were 10 for influenza, two for RSV and 50 for COVID-19.
Community-acquired emergency inpatient numbers for influenza and RSV remained low and stable, while COVID-19 has increased (Figure 5.6).
Community-acquired emergency inpatient numbers by age group over the previous year are shown in Figure 5.7.
Methods
Presentation of data
Unless otherwise stated, data are presented using epidemiological weeks (a standardised method of counting weeks [Monday-Sunday] to allow for the comparison of data year after year). This is dependent on the data available. The data included in this report are the most up to date data available at the time of the report; however, this is subject to change as the data are subject to ongoing quality assurance.
Virology surveillance
All virology data provided here are preliminary. Virology data for prior weeks, as included in this or future reports, are subject to updates based on laboratory returns received after the last report was produced. The report offers the most up-to-date information available.
Rates per 100,000 population are calculated using the NISRA 2024 Mid-Year Population Estimates.
Episodes of infection
Influenza
Influenza episodes are defined by a 42-day (6-week) period from the date of the first positive test result (utilising any test method, including PCR and Point of Care Tests, or source of sample, including hospital, GP, other source), with the episode beginning with the earliest positive specimen date. Subsequent positive specimen dates for the same individual within 42 days of the last are included in the one episode. Positive specimens for the same individual more than 42 days after the last are counted in a separate episode.
RSV
RSV episodes are defined by a 14-day (2-week) period from the date of the first positive test result (utilising any test method, including PCR and Point of Care Tests, or source of sample, including hospital, GP, other source), with the episode beginning with the earliest positive specimen date. Subsequent positive specimen dates for the same individual within 14 days of the last are included in the one episode. Positive specimens for the same individual more than 14 days after the last are counted in a separate episode.
COVID-19
COVID-19 episodes are defined by a 90-day period from the date of the first positive test result (utilising any test method, including PCR and Point of Care Tests, or source of sample, including hospital, GP, other source), with the episode beginning with the earliest positive specimen date. Subsequent positive specimen dates for the same individual within 90 days of the last are included in the one episode. Positive specimens for the same individual more than 90 days after the last are counted in a separate episode.
Testing and positivity (%)
Influenza, RSV, COVID-19, rhinovirus, adenovirus, parainfluenza and human metapneumovirus
Instead of utilising an episode-based approach, the data is analysed on an epidemiological week basis. Within each epidemiological week, an individual is limited to one influenza test, whether positive or negative. If an individual tests positive for influenza during a specific epidemiological week and subsequently tests positive again within the same week, the second positive test is not counted. Regardless of whether it occurs before or after a negative test within the same epidemiological week, a positive test always takes precedence and is recorded. Similarly, only the first test of multiple negative results is counted for each individual within any given epidemiological week. This helps prevent the double-counting of tests, particularly for individuals who may be hospitalised and routinely tested.
Weekly test positivity is calculated as the proportion of positive tests to total tests conducted. To estimate the uncertainty around these proportions, 95% confidence intervals (CIs) were computed using the Wilson score interval. The Wilson method is a binomial proportion CI that avoids the limitations of some other methods, particularly for small sample sizes or extreme proportions. It provides more accurate bounds by incorporating the standard error and adjusting for asymmetry in the binomial distribution. This method ensures that the plotted CIs reflect the true statistical uncertainty in weekly positivity estimates.
The same methodology is applied when analysing RSV, COVID-19, rhinovirus, adenovirus, parainfluenza and human metapneumovirus data.
Sentinel surveillance
The Public Health Agency works with GPs to deliver a community-based surveillance programme for respiratory infections in Northern Ireland. The programme provides valuable intelligence about the circulation of respiratory viruses in Northern Ireland to inform health and social care system planning and preparedness. Participation involves taking nasal/throat swabs from some symptomatic patients who agree to have a swab, and who attend (in person) with ILI, ARI or suspected COVID-19. Testing is opportunistic and within 10 days of symptom onset. Swabs are tested for influenza, RSV and COVID-19 at the RVL and surveillance is year-round.
SARS-CoV-2 genomics
A subset of SARS-CoV-2 positive PCR samples are sent to sequencing laboratories in Belfast Health and Social Care Trust and Queen’s University Belfast for sequencing. On 29th November 2022 the lineage assignment algorithm was switched from PangoLEARN to UShER for lineage counts. PangoLEARN uses a machine learning algorithm, whereas UShER uses phylogenetic placement and produces fewer unassigned lineages. This switch has been applied retrospectively, therefore total counts for all lineages have been affected. A more detailed COVID-19 Genomics Bulletin containing a further breakdown of sub-lineages is published weekly.
Primary care surveillance
Consultation rates for influenza/influenza-like-illness (‘flu/ILI’), acute respiratory infection (ARI) and COVID-19
GP in-hours consultation data with 100% coverage of the Northern Ireland population is auto-extracted weekly from the General Practitioner Intelligence Platform (GPIP). This data includes weekly aggregate consultations for ‘flu/ILI’, ARI, and COVID-19, and includes weekly registered patients. The data is available for different Health and Social Care Trusts, and by age and sex.
Secondary care surveillance
Influenza and RSV
Community-acquired influenza and RSV emergency admissions to acute hospitals are estimated by combining data from the Patient Administration System (PAS), EPIC and virological reports in the Northern Ireland Health Analytics Platform (NIHAP). Admissions are counted where there was a positive test up to seven days before admission or up to one day after admission, and the method of admission was ‘Emergency’. The number of inpatients is counted at midnight. Admissions and occupancy refer to the first admission per infection episode.
COVID-19
Community-acquired COVID-19 emergency admissions to acute hospitals are estimated by combining data from the PAS, EPIC and virological reports in NIHAP. Admissions are counted where there was a positive PCR or lateral flow test up to 14 days before admission or up to one day after admission., and the method of admission was ‘Emergency’. The number of inpatients is counted at midnight. Admissions and occupancy refer to the first admission per infection episode. The method used in this report is different to that previously reported by the Department of Health’s COVID-19 dashboard, which used administrative coding to identify COVID-19 admissions.
Mortality surveillance
NISRA death statistics are published weekly, and include weekly counts of deaths related to influenza and/or pneumonia (from 31 January 2025), and deaths related to COVID-19. This enables comparisons with weekly information published by the Office for National Statistics (ONS) covering England and Wales.
The statistics report on deaths where influenza and/or pneumonia, or COVID-19, was mentioned anywhere on the death certificate. As a result, the counts will reflect deaths where these diseases have contributed to a death but were not necessarily the underlying cause of the death.
