Integrated Respiratory Virus Bulletin, Ireland

Week 3 2025 (12/01/2025 - 19/01/2025)

Report prepared on 23/01/2025



This interactive bulletin reports on the latest epidemiology of COVID-19, influenza, respiratory syncytial virus (RSV) and other respiratory viruses (ORVs) in Ireland. HPSC monitors several integrated respiratory virus surveillance systems that are included in this bulletin. This report will be published weekly during the winter season (week 40 to week 20).

How to use this interactive bulletin

For interactive graphs – data values and labels can be seen by hovering over graph lines or bars. Specific categories can be selected or deselected by clicking on the relevant category in the legend. Readers can skip to specific sections by clicking on the table of contents to the left of the screen.

1 Key messages

During week 3 2025, influenza activity in Ireland remained at high levels, although notified influenza cases, hospitalisations and hospital bed occupancy have decreased during the last two weeks. Sentinel GP influenza positivity declined during the last three weeks, but remained above the 10% positivity threshold at 41.1%. Influenza A(H1)pdm09 is the predominant influenza virus circulating, with influenza A(H3) and B virus detections reported at lower levels. RSV notifications and hospitalisations remained stable in week 3 2025, however decreased in those aged less than one year and increased in those aged 80 years and older. COVID-19 activity remained at low levels during week 3 2025.

1.1 Summary for week 3 2025

Primary Care Surveillance

The sentinel GP Acute Respiratory Infection (ARI) consultation rate remained high, however decreased in week 3 2025, for the second consecutive week, to 126.9/100,000 population. The highest rates were in those aged <5 years at 241.4/100,000 population, a substantive decrease from the week 51 2024 peak of 729.1/100,000 population. Sentinel GP influenza positivity declined for the third week in a row, to 41.1%, but remained above the 10% positivity threshold levels. Sentinel GP RSV positivity was 10.1%, at the baseline threshold. All other seasonal respiratory pathogens are circulating at lower levels. The proportion of GP-OOH calls for self-reported cough and flu calls were above threshold levels for almost all age groups (except for flu calls in those aged 0 to 4 years) in week 3 2025.

COVID-19

COVID-19 activity remained at low levels across all indicators in week 3 2025, with a decrease in case numbers and hospitalisations compared to week 2. COVID-19 cases decreased by 18.3%, from 180 cases notified in week 2 to 147 cases in week 3. Hospitalised cases decreased by 12.3%, with 57 cases in week 2 compared to 50 cases in week 3. ICU admissions and deaths remained low. XEC was the dominant SARS-CoV-2 variant and accounted for 64.1% of samples sequenced between weeks 48 and 52 2024.

Influenza

Influenza activity decreased in week 3 2025, for the second consecutive week, but is still circulating at high levels. The number of notified influenza cases decreased by 30% to 2,522 cases in week 3 2025, compared to 3,619 reported in in week 2 2025.The overall notification rate was 49.0/100,000 population and was highest in those aged ≥80 years at 244.7/100,000 population, followed by those aged less than one year at 135.0/100,000 population. There were 524 hospitalisations, eight ICU admissions and four deaths notified during week 3 2025. For the season to date (weeks 40 2024 to week 3 2025), 150 ICU admissions and 94 deaths have been reported. Influenza hospital bed occupancy decreased during week 3 2025. Influenza A(H1)pdm09 is the predominant virus circulating this season, followed by influenza B and influenza A(H3). Influenza B notified cases remain at low levels, however, have increased in recent weeks. Among all notified influenza cases during week 3 2025, 14.8% (373) were influenza B.

RSV

The number of notified RSV cases remained stable in week 3 2025, with 594 cases notified compared to 575 in week 2 2025. The overall notification rate was 11.5/100,000 population. In week 3 2025, the notification rate decreased for the second consecutive week, in those aged less than one year to 179.9/100,000 population, and increased in those aged 80 years and older to 70.7/100,000 population. There were 153 hospitalisations and no ICU admissions in week 3 2025. For the season to date, 62 ICU admissions and three deaths have been reported (weeks 40 2024-3 2025).

Severe Acute Respiratory Infection (SARI)

Based on the data from two sentinel hospital sites (SJH & UHL), the number of SARI cases reported increased slightly among cases aged <15 years, with 24 cases reported, compared to 21 cases in week 2 2025. However, a decrease was observed among SARI cases aged ≥15 years, with 37 cases reported compared to 40 cases in week 2 2025. In week 3 2025, influenza positivity decreased to 37.7% from 44% in week 2 2025; RSV positivity also decreased to 11.5% from 14%. SARS-CoV-2 positivity remained at low levels increasing to 3.3% from 0% in week 2 2025.

Outbreaks

COVID-19 outbreaks remained stable between week 2 and week 3, 2025. A total of five COVID-19 outbreaks were reported during week 3, including four in hospitals and one in a residential institution. Forty-six influenza outbreaks (18 in hospitals, 19 in nursing homes and eight in residential institutions) were reported in week 3, a decrease from 53 outbreaks in week 2. Eight RSV outbreaks (three in hospitals and five in nursing homes) and ten other ARI outbreaks (nine in nursing homes and one in a residential institution) were also notified during week 3 2025.


2 Activity

2.1 Confirmed Cases


1: Number of notified cases of laboratory confirmed of COVID-19, influenza and RSV by notification week in Ireland between week 40 2023 and week 3 2025. Data source: CIDR


2.2 COVID-19 seasonal trends

2: Number of notified cases of laboratory confirmed of COVID-19 by notification week in Ireland between week 40 2019 and week 3 2025. Data source: CIDR

Please note: where there is a 53 week year, the average of week 52 and week 53 is taken.


2.3 Influenza seasonal trends

3: Number of notified cases of laboratory confirmed of influenza by notification week in Ireland between week 40 2019 and week 3 2025. Data source: CIDR

Please note: where there is a 53 week year, the average of week 52 and week 53 is taken.


2.4 RSV seasonal trends

4: Number of notified cases of laboratory confirmed RSV by notification week in Ireland between week 40 2019 and week 3 2025. Data source: CIDR

Please note: where there is a 53 week year, the average of week 52 and week 53 is taken.


Table 1: Number and incidence of notified laboratory confirmed cases of COVID-19, influenza and RSV, by age, sex and HSE health region, Ireland, week 3 2025. Data source: CIDR.

Number of cases (incidence per 100,000 population)

All pathogens

COVID-19

Influenza

RSV

Cases

3,263 (63.4)

147 (2.9)

2,522 (49.0)

594 (11.5)

Age groups (years)

<1

189 (327.0)

7 (12.1)

78 (135.0)

104 (179.9)

1-4

398 (167.5)

4 (1.7)

299 (125.8)

95 (40.0)

5-14

235 (32.8)

3 (0.4)

214 (29.9)

18 (2.5)

15-44

664 (32.1)

17 (0.8)

573 (27.7)

74 (3.6)

45-64

562 (43.5)

22 (1.7)

467 (36.1)

73 (5.6)

65-79

583 (97.9)

35 (5.9)

446 (74.9)

102 (17.1)

>80

630 (348.0)

59 (32.6)

443 (244.7)

128 (70.7)

Median age (IQR)

51 (14-76)

75 (54-85)

49 (17-74)

48 (1-77)

Sex

Male

1,547 (60.8)

80 (3.1)

1,175 (46.2)

292 (11.5)

Female

1,702 (65.3)

67 (2.6)

1,334 (51.2)

301 (11.6)

HSE Health Regions

Dublin and North East

1,182 (23)

35 (2.9)

967 (81.5)

180 (15.2)

Dublin and Midlands

519 (10.1)

24 (2.2)

378 (35.1)

117 (10.9)

Dublin and South East

552 (10.7)

24 (2.5)

432 (44.5)

96 (9.9)

South West

373 (7.2)

17 (2.3)

283 (38.2)

73 (9.9)

Mid West

210 (4.1)

14 (3.4)

154 (37.3)

42 (10.2)

West and North West

424 (8.2)

33 (4.3)

306 (40.3)

85 (11.2)


An overview of the characteristics of all cases reported since the start of the season is presented in Appendix A1.


5: Incidence of notified cases of laboratory-confirmed COVID-19, influenza and RSV by HSE Health Region for the last 12 weeks, from week 44 2024 to week 3 2025. Data source: CIDR


6: Age and sex-specific incidence of notified cases of laboratory confirmed COVID-19, influenza and RSV from week 40 2024 to week 3 2025. Data source: CIDR

Please note that the scale on the x-axis may differ by pathogen, to account for differences in the number of cases notified for each pathogen.


7: Incidence of notified cases of laboratory confirmed COVID-19, influenza and RSV by age group from week 40 2023 to week 3 2025. Data source: CIDR


2.5 Sentinel GP Acute Respiratory Infection (ARI) Surveillance

2.5.1 Sentinel GP ARI

8: Sentinel GP ARI consultation rate per 100,000 population overall (with associated number of influenza, RSV and SARS-CoV-2 positive sentinel GP ARI specimens) from week 40 2023 to week 3 2025. Data source: Sentinel GP surveillance system and NVRL.

2.5.2 Sentinel GP ARI by Age Group

9: Sentinel GP ARI consultation incidence by age-group, from week 40 2023 to week 3 2025 2024. Data source: Sentinel GP surveillance system.


2.6 GP Out-of-Hours Surveillance


10: Percentage of calls to GP Out-of-Hours services for self-reported cough and self-reported flu, for all ages and by age-group, by week of call from week 40 2023 to week 3 2025. Data source: Participating GP Out-of-Hours services in Ireland.


3 Severity and Impact

3.1 Emergency Department Cases

3.1.1 Incidence of Emergency Department Cases

11: Incidence of emergency department cases of laboratory confirmed COVID-19, influenza and RSV from week 40 2023 to week 3 2025. Data source: CIDR


3.1.2 Number of Emergency Department Cases


12: Number of emergency department cases of laboratory confirmed COVID-19, influenza and RSV, from week 40 2023 to week 3 2025. Data source: CIDR


3.2 Hospital Admissions

3.2.1 Incidence of Hospitalised Cases


13: Incidence of hospitalised cases of laboratory confirmed COVID-19, influenza and RSV from week 40 2023 to week 3 2025. Data source: CIDR


3.2.2 Number of Hospitalised Cases


14: Number of hospitalised cases of laboratory confirmed COVID-19, influenza and RSV from week 40 2023 to week 3 2025. Data source: CIDR

Table 2: Number and incidence of hospitalised cases of laboratory confirmed COVID-19, influenza and RSV by age, sex and HSE health region, Ireland, week 3 2025. Data source: CIDR

Number of cases (incidence per 100,000 population)

All pathogens

COVID-19

Influenza

RSV

Cases

727 (14.1)

50 (1.0)

524 (10.2)

153 (3.0)

Age groups (years)

<1

48 (83.1)

1 (1.7)

18 (31.1)

29 (50.2)

1-4

86 (36.2)

1 (0.4)

61 (25.7)

24 (10.1)

5-14

47 (6.6)

2 (0.3)

39 (5.4)

6 (0.8)

15-44

68 (3.3)

4 (0.2)

53 (2.6)

11 (0.5)

45-64

108 (8.4)

4 (0.3)

85 (6.6)

19 (1.5)

65-79

153 (25.7)

11 (1.8)

113 (19.0)

29 (4.9)

>80

216 (119.3)

27 (14.9)

154 (85.1)

35 (19.3)

Median age (IQR)

67 (15.25-81)

82 (72.25-86.75)

67 (27-81)

51 (1-78)

Sex

Male

342 (13.4)

29 (1.1)

236 (9.3)

77 (3.0)

Female

384 (14.7)

21 (0.8)

287 (11.0)

76 (2.9)

HSE Health Regions

Dublin and North East

145 (2.8)

4 (0.3)

118 (9.9)

23 (1.9)

Dublin and Midlands

81 (1.6)

7 (0.6)

51 (4.7)

23 (2.1)

Dublin and South East

143 (2.8)

10 (1)

96 (9.9)

37 (3.8)

South West

108 (2.1)

7 (0.9)

78 (10.5)

23 (3.1)

Mid West

93 (1.8)

8 (1.9)

65 (15.7)

20 (4.8)

West and North West

157 (3)

14 (1.8)

116 (15.3)

27 (3.6)


An overview of the characteristics of all hospitalised cases reported since the start of the season is presented in Appendix A2.


15: Age and sex-specific incidence of hospitalised cases of laboratory-confirmed COVID-19, influenza and RSV from week 40 2024 to week 3 2025. Data source: CIDR

Please note that the scale on the x-axis may differ by pathogen, to account for differences in the number of cases notified for each pathogen.


16: Incidence of hospitalised cases of laboratory confirmed COVID-19, influenza and RSV by age group from week 40 2023 to week 3 2025. Data source: CIDR


Figure 17: Cumulative incidence of hospitalised cases of laboratory confirmed COVID-19, influenza and RSV by HSE health region, according to patient county of residence in week 3 2025. Data source: CIDR


3.2.3 Bed Occupancy in Acute Inpatient Settings


18: Number of hospital beds occupied by patients with laboratory confirmed COVID-19, influenza or RSV. Data source: HSE Planning and Performance Unit


3.3 ICU Admissions


19: Number of ICU admissions due to laboratory-confirmed COVID-19, influenza and RSV, week 40 2023 to week 3 2025. Data source: CIDR


Please note that there may be a delay in documenting ICU cases on Ireland’s Computerised Infectious Disease Reporting System (CIDR) system and submitting enhanced ICU surveillance data, consequently numbers reported for the most recent weeks may be incomplete.

Table 3: Number and incidence of ICU admissions due to COVID-19, influenza and RSV, week 3 2025, and season to date (from week 40 2024). Data source: CIDR.

Week 3, 2025

Season to date

Number of ICU admissionsa

ICU admissions per 1,000 hospitalisations

% of hospitalised cases admitted to ICU

Number of ICU admissions

ICU admissions per 1,000 hospitalisations

% of hospitalised cases admitted to ICU

COVID-19

0

0.0

0.0

32

23.3

2.3

Influenza

8

15.3

1.5

150

36.0

3.6

RSV

0

0.0

0.0

62

35.9

3.6

aICU admissions include all cases admitted to ICU due to COVID-19, influenza and RSV.


3.4 Sentinel Severe Acute Respiratory Infection (SARI) Surveillance


20: Number and incidence of SARI hospitalised cases (emergency admissions) by week of hospital admission, from week 40 2024 to week 3 2025. Data source: Sentinel SARI surveillance system.


21: Percentage of SARI cases with a positive laboratory test result for SARS-CoV-2, influenza or RSV by week, from week 40 2024 to week 3 2025. Data source: Sentinel SARI surveillance system.


3.5 Mortality

3.5.1 Deaths Among Confirmed Cases


22: Number of COVID-19, influenza and RSV deaths by week of death. Data source: CIDR


Table 4: Number and incidence of COVID-19, influenza and RSV deaths for the season to date. Data source: CIDR

COVID-19

Influenza

RSV

Age (years)

Number

Incidence per 100,000 population

Number

Incidence per 100,000 population

Number

Incidence per 100,000 population

<65

4

0.1

15

0.3

0

0.0

>65

60

7.7

79

10.2

3

0.4

Total

64

1.2

94

1.8

3

0.1


4 Outbreaks


23: Number of COVID-19, influenza, RSV and other ARI outbreaks reported in health and care settings from week 40 2023 to week 3 2025. Data source: CIDR.


Table 5 : COVID-19, influenza, RSV and other ARI outbreaks reported by setting week 3 2025. Data source: CIDR

Epi week: 3 2025

Outbreak location

COVID-19

Influenza

RSV

ARI

Total week 3, 2025

Total season to date

Comm. Hosp/Long-stay unit

0

0

0

0

0

43

Hospital

4

18

3

0

25

219

Nursing home

0

19

5

9

33

261

Other healthcare service

0

0

0

0

0

10

Residential institution

1

8

0

1

10

68

Total Health Care Settings

5

45

8

10

68

601

Total Non Health Care Settings

0

1

0

0

1

8

Total

5

46

8

10

69

610


24: Number of COVID-19, influenza, RSV and other ARI outbreaks by HSE health region, week 3 2025. Data source: CIDR.


5 Virology and Genomic Surveillance

5.1 Virus Positivity and Dominant Virus Types/subtypes in Circulation


Table 6: Number and percentage positive SARS-CoV-2, influenza and RSV specimens by surveillance source, week 3 2025. Data source: CIDR, National Virus Reference Laboratory (NVRL).

SARS-CoV-2

Influenza

RSV

Surveillance system

Total tested

Total positive

% positive

Total positive

% positive

Total positive

% positive

NVRL Sentinel GP ARI

141

4

2.8

58

41.1

10

7.1

NVRL nonsentinel respiratory viruses

376

12

3.2

82

21.8

38

10.1


25: Percentage for sentinel GP ARI specimens and non-sentinel respiratory specimens testing positive for SARS-CoV-2, influenza, RSV and other respiratory viruses, by week of specimen collection, week 20 2024 to week 3 2025. PIV = parainfluenza viruses. Data source: NVRL


26: Number of sentinel GP ARI and non-sentinel respiratory influenza positive specimens, and laboratory confirmed influenza notifications by influenza type/sub-type, by week of specimen collection, week 40 2023 to week 3 2025. Data source: NVRL, CIDR


Underlying data on the total number of tests, total number of positives and percentage positive by week and for the season to date for each virus for both sentinel and non-sentinel specimens are presented in Appendix A3, Appendix A4, Appendix A5, Appendix A6


5.2 SARS-CoV-2 Genetic and Antigenic Data Including Whole Genome Sequencing


27: SARS-CoV-2 whole genome sequencing results, specimen collection dates from week 40 2023 to week 52 2024


There is typically a lag time of 1-3 weeks between a case being notified, selected for sequencing and sequencing being completed. Therefore the percentage of cases notified in this time period who are ultimately sequenced will be higher than reported here.


28: SARS-CoV-2 whole genome sequencing results by week specimen collected from week 48 2024 to week 52 2024


6 SARS-CoV-2 Wastewater Surveillance


29: Approximate location of wastewater catchment areas and SARS-CoV-2 viral loads (gc/day) in wastewater and percentage change compared to previous week, National Wastewater Surveillance Programme, week 50 2024


Figure 30: Weekly distribution of population-normalised SARS-CoV-2 viral load (gc/day/person), National Wastewater Surveillance Programme, May 2021 to week 50 2024


9 Technical notes

General

Data are provisional and subject to ongoing review, validation and update. As a result, figures in this report may differ from previously published figures.

The weekly calendar runs from Sunday to Saturday for respiratory virus notifications on CIDR (as per the Infectious Disease Regulations 1982 and subsequent amendments) and Monday to Sunday for the sentinel GP and SARI surveillance systems (as per ISO week). Further information on epidemiological dates and weeks can be found on the HPSC website.

Definitions

The case definitions for COVID-19, influenza and RSV are available here. Only data on laboratory-confirmed cases, including cases diagnosed using near patient molecular tests, are included in this report.

Sentinel GP ARI consultations are consultations to sentinel GP practices for Acute Respiratory Infection (ARI), with ARI defined as Sudden onset of symptoms AND at least one of the following four respiratory symptoms: Cough, sore throat, shortness of breath, coryza AND a clinician’s judgement that the illness is due to an infection.

GP out of hours calls refer to calls to GP out of hours services from persons with self-reported clinical symptoms of ‘flu’ or ‘cough’.

Emergency Department cases refer to cases treated in emergency departments, with no indication on CIDR that they have subsequently been admitted to hospital.

Hospitalised cases are inpatients with laboratory confirmed SARS-CoV-2, influenza or RSV and includes inpatients with incidental infections, where the infection is not the reason for their admission.

Bed occupancy refers to the number of laboratory confirmed cases admitted to acute inpatient sites at 08:00 hrs on the day of reporting.

A SARI case is defined as a person hospitalised for at least 24 hours with acute respiratory infection, with at least one of the following symptoms: cough, fever, shortness of breath OR sudden onset of anosmia, ageusia or dysgeusia with onset of symptoms within 14 days prior to hospital admission. A SARI case refers to an individual patient episode of care.

As of September 2024, ICU admissions for COVID-19, influenza and RSV refer to those admitted to intensive care where COVID-19, influenza or RSV were the primary or contributory cause of admission. Prior to September 2024, ICU admissions for influenza and RSV included all admissions where the patient tested positive for influenza or RSV, irrespective of whether these pathogens were the cause of admission.

COVID-19, influenza and RSV deaths are defined as a death in a person with laboratory confirmed COVID-19, influenza or RSV infection see case definitions (this includes cases detected postmortem) and where COVID-19, influenza or RSV is reported in any of the four cause of death fields on the death certificate. Deaths where there is a clear alternative cause of death (e.g. trauma, suicide) are not recorded as COVID-19/influenza/RSV deaths. Deaths where there is a period of complete recovery (as assessed by a clinician) between a COVID-19, influenza or RSV episode of illness and death, are also not recorded as deaths.

Test Positivity: Positive tests refer to all positive specimens and includes duplicates and individuals who were re-tested.

Outbreaks are defined as two or more cases of acute respiratory infection with the same pathogen (SARS-CoV-2, influenza or respiratory syncytial virus (RSV)) confirmed by a laboratory test or near patient test carried out by a health professional, and where there is reason to consider that these cases may be epidemiologically linked in place and time.

Other Acute Respiratory Infection (ARI) outbreaks are defined as: Two or more cases of acute respiratory infection arising within the same 48hr period epidemiologically linked in place: Outbreaks are classified as Suspect ARI outbreaks, where testing has not been completed, is pending or has been negative for Influenza, RSV and SARS-CoV-2. Outbreaks are classified as confirmed if other respiratory pathogens (ORVs), e.g. Rhinovirus, hMPV, Coronavirus OC43 etc are identified via laboratory confirmation. The outbreak data presented in this report includes both confirmed and suspect outbreaks.

Variant working definitions for ‘SARS-CoV-2 variants of concern’ (VOC), ‘SARS-CoV-2 variants of interest’ (VOI) and ‘SARS-CoV-2 variants under monitoring’ (VUM) are available on the WHO website and ECDC website.

Data Sources

The Computerised Infectious Disease Reporting (CIDR) system: CIDR is the source of statutory notification data on laboratory-confirmed COVID-19, influenza, RSV (including data on notified, emergency department, hospitalised and ICU cases and data on cases who died) and data on outbreaks.

The type/subtype of laboratory confirmed influenza notifications are reported on the CIDR system. The number of cases hospitalised and admitted to ICU described in this report relate only to cases notified during this reporting period, with known hospitalisation/ICU status at the time of reporting.

Regional Departments of Public Health currently prioritise the investigation and reporting of outbreaks in settings that benefit most from public health and clinical intervention. The outbreak data reported here focuses on these key settings/groups. These settings include acute hospitals, nursing homes, community hospital/long-stay units, residential institutions (centres for disabilities, centres for older people, children’s/TUSLA residential centres and mental health facilities) and other healthcare settings.

Population denominator data for analyses of CIDR data on notified, emergency department, hospitalised and ICU cases and deaths are taken from Census 2022.

Sentinel GP surveillance system: This includes 100 participating general practices (located in all HSE Health Regions). These practices report electronically on a weekly basis, the number of patients who consulted with acute respiratory infection (ARI) and influenza-like illness (ILI) (identified using International Classification of Primary Care 2 codes R74 and R80). These practices provide overall and age-stratified denominator data on the number of registered patients who have sought care at the practice during the previous three years. The combined patient population in these practices is estimated to be approximately 10% of the national population. Sentinel GPs take a combined nose and throat swab from the first five patients attending their practice each week who meet the ARI case definition and send these to the NVRL for testing.

GP Out-of-hours (GPOOHs) services: Five out of 14 GPOOHs services provide weekly data on the total and age-stratified number of out of hours calls for 1) all reasons, 2) for self-reported cough and 3) for self-reported flu. The denominator for calculations of percentage of calls is the total number of calls for all reasons.

The HSE Performance Management and Improvement Unit (PMIU) provides daily data on bed occupancy (the number of currents inpatients with laboratory confirmed COVID-19, influenza and RSV).

Severe Acute Respiratory Infections (SARI) surveillance system: SARI cases are identified from new admissions through the Emergency Department, based on clinical symptoms. Patients that develop SARI during their admission, or who are admitted through alternate routes, are not included.

National Virus Reference Laboratory (NVRL): The NVRL routinely test sentinel GP and non-sentinel respiratory specimens for SARS-CoV-2, influenza, RSV and a panel of other seasonal respiratory viruses (ORV). The NVRL report on influenza type/subtype of sentinel GP ARI and non-sentinel respiratory specimens on a weekly basis.

As of 14/10/2024 HPSC has ceased reporting on detections of hMPV from virological surveillance of sentinel and non-sentinel specimens. This is due to an increased risk of false positive results from the routine respiratory panel.

National SARS-CoV-2 Whole Genome Sequencing Surveillance Programme (NSWGSSP): The SARS-CoV-2 sequencing sampling framework currently focuses on notified COVID-19 cases with severe disease (hospitalisation, ICU admission) and deaths, COVID-19 outbreaks in health and care settings, sentinel surveillance programmes in the community and acute hospitals and targeted sequencing based on public health risk assessment/clinical requests and virological changes e.g. new variant of concern. There is typically a lag time of 1-3 weeks between a COVID-19 case being notified, selected for sequencing and SARS-CoV-2 sequencing being completed. Therefore, the proportion of notified COVID-19 cases notified in this time period from whom specimens are ultimately sequenced will be higher than currently reported here. The HPSC link sequencing results received from laboratories to epidemiological data on COVID-19 cases reported on the CIDR system. This report summarises WGS results and epidemiological data for COVID-19 cases that have been sequenced in Ireland since week 40 2023 (specimen dates between 01/10/2023 and 28/12/2024). The SARS-CoV-2 sequencing results included in this report reflect all data available as of 16/01/2025.

National SARS-CoV-2 Wastewater Surveillance Programme: A detailed description of the process involved for wastewater collection, sampling and analyses is available in the routinely published national SARS-CoV-2 wastewater surveillance programme reports available here


10 Appendix

Appendix Table 1: Notified laboratory confirmed cases of COVID-19, influenza and RSV by age, sex and HSE health region, from week 40 2024, to week 3 2025. Data source: CIDR.

Number of cases (incidence per 100,000 population)

All pathogens

COVID-19

Influenza

RSV

Cases

25,745 (500.0)

3,415 (66.3)

17,164 (333.3)

5,166 (100.3)

Age groups (years)

<1

2,020 (3,495.1)

156 (269.9)

550 (951.6)

1,314 (2,273.5)

1-4

3,925 (1,651.8)

91 (38.3)

2,094 (881.2)

1,740 (732.3)

5-14

1,971 (274.9)

46 (6.4)

1,692 (236.0)

233 (32.5)

15-44

4,523 (218.8)

482 (23.3)

3,717 (179.8)

324 (15.7)

45-64

4,320 (334.0)

601 (46.5)

3,339 (258.2)

380 (29.4)

65-79

4,638 (779.1)

915 (153.7)

3,134 (526.5)

589 (98.9)

>80

4,344 (2,399.6)

1,123 (620.3)

2,635 (1,455.6)

586 (323.7)

Median age (IQR)

47 (6-74)

72 (48-83)

48 (14-72)

2 (0-60)

Sex

Male

12,218 (480.2)

1,616 (63.5)

8,068 (317.1)

2,534 (99.6)

Female

13,482 (517.6)

1,798 (69.0)

9,063 (348.0)

2,621 (100.6)

HSE Health Regions

Dublin and North East

6,247 (121.3)

782 (65.9)

4205 (354.2)

1260 (106.1)

Dublin and Midlands

4,575 (88.8)

600 (55.7)

2974 (276)

1001 (92.9)

Dublin and South East

5,580 (108.4)

822 (84.6)

3819 (393.3)

939 (96.7)

South West

3,342 (64.9)

476 (64.3)

2330 (314.6)

536 (72.4)

Mid West

1,879 (36.5)

298 (72.1)

1348 (326.3)

233 (56.4)

West and North West

4,115 (79.9)

437 (57.5)

2482 (326.7)

1196 (157.4)


Appendix Table 2: Hospitalised laboratory confirmed cases of COVID-19, influenza and RSV by age, sex and HSE health region from week 40 2024 to week 3 2025. Data source: CIDR.

Number of cases (incidence per 100,000 population)

All pathogens

COVID-19

Influenza

RSV

Cases

7,266 (141.1)

1,371 (26.6)

4,169 (81.0)

1,726 (33.5)

Age groups (years)

<1

718 (1,242.3)

59 (102.1)

173 (299.3)

486 (840.9)

1-4

1,221 (513.8)

35 (14.7)

573 (241.1)

613 (258.0)

5-14

560 (78.1)

26 (3.6)

439 (61.2)

95 (13.3)

15-44

676 (32.7)

119 (5.8)

485 (23.5)

72 (3.5)

45-64

1,002 (77.5)

216 (16.7)

687 (53.1)

99 (7.7)

65-79

1,505 (252.8)

397 (66.7)

923 (155.1)

185 (31.1)

>80

1,583 (874.5)

519 (286.7)

888 (490.5)

176 (97.2)

Median age (IQR)

56 (4-78)

75 (58-84)

58 (9-78)

2 (0-54)

Sex

Male

3,602 (141.6)

706 (27.7)

2,036 (80.0)

860 (33.8)

Female

3,659 (140.5)

665 (25.5)

2,129 (81.7)

865 (33.2)

HSE Health Regions

Dublin and North East

905 (17.6)

180 (15.2)

511 (43)

214 (18)

Dublin and Midlands

1,162 (22.6)

267 (24.8)

551 (51.1)

344 (31.9)

Dublin and South East

1,600 (31.1)

267 (27.5)

923 (95)

410 (42.2)

South West

1,110 (21.6)

238 (32.1)

688 (92.9)

184 (24.8)

Mid West

904 (17.6)

162 (39.2)

600 (145.3)

142 (34.4)

West and North West

1,584 (30.8)

257 (33.8)

895 (117.8)

432 (56.9)


Appendix Table 3: Number and percentage positive Sentinel GP ARI specimens by respiratory virus for week 2 2025, week 3 2025 and the 2024/2025 season. Data source: NVRL.

Week 2 2025 (N = 252)

Week 3 2025 (N = 141)

2024/2025 (N = 2522)

Virus

Total positive

% positive

Total positive

% positive

Total positive

% positive

SARS-CoV-2

3

1.2

4

2.8

75

3.0

Influenza Virus

116

46.0

58

41.1

719

28.5

Respiratory Syncytial Virus (RSV)

21

8.3

10

7.1

126

5.0

Rhino/enterovirus

16

6.3

10

7.1

418

16.6

Adenovirus

0

0.0

0

0.0

12

0.5

Bocavirus

0

0.0

0

0.0

7

0.3

Parainfluenza virus type 1 (PIV-1)

1

0.4

0

0.0

36

1.4

Parainfluenza virus type 2 (PIV-2)

0

0.0

0

0.0

35

1.4

Parainfluenza virus type 3 (PIV-3)

0

0.0

0

0.0

10

0.4

Parainfluenza virus type 4 (PIV-4)

0

0.0

0

0.0

27

1.1


Appendix Table 4: Number and percentage positive NVRL non-sentinel respiratory specimens by respiratory virus, week 2 2025, week 3 2025 and the 2024/2025 season. Data source: NVRL.

Week 2 2025 (N = 624)

Week 3 2025 (N = 376)

2024/2025 (N = 5644)

Virus

Total positive

% positive

Total positive

% positive

Total positive

% positive

SARS-CoV-2

18

2.9

12

3.2

142

2.5

Influenza Virus

193

30.9

82

21.8

1,630

28.9

Respiratory Syncytial Virus (RSV)

67

10.7

38

10.1

452

8.0

Rhino/enterovirus

32

5.1

26

6.9

578

10.2

Adenovirus

1

0.2

1

0.3

35

0.6

Bocavirus

1

0.2

3

0.8

37

0.7

Parainfluenza virus type 1 (PIV-1)

3

0.5

1

0.3

50

0.9

Parainfluenza virus type 2 (PIV-2)

3

0.5

1

0.3

41

0.7

Parainfluenza virus type 3 (PIV-3)

1

0.2

1

0.3

9

0.2

Parainfluenza virus type 4 (PIV-4)

1

0.2

0

0.0

45

0.8


Appendix Table 5: Influenza type and sub-type distribution among sentinel GP ARI and non-sentinel respiratory influenza positive specimens for week 2 2025, week 3 2025 and the 2024/2025 season. Data source: NVRL.

Influenza A

Influenza B

Time period

Specimen source

Total influenza positive

Total

A(H1)pdm09

A(H3)

A(not subtyped)

Total

B Victoria

B (upspecified)

Week 2 2025

Sentinel GP ARI

116

81

67

8

6

35

0

35

Non-sentinel respiratory

193

174

148

10

16

19

0

19

Total

309

255

215

18

22

54

0

54

Week 3 2025

Sentinel GP ARI

58

39

28

7

4

19

0

19

Non-sentinel respiratory

82

68

52

6

10

14

0

14

Total

140

107

80

13

14

33

0

33

Season to date

Sentinel GP ARI

719

595

473

58

64

124

0

124

Non-sentinel respiratory

1,630

1,510

1,265

120

125

120

20

100

Total

2,349

2,105

1,738

178

189

244

20

224


Appendix Table 6: RSV type distribution among sentinel GP ARI and non-sentinel respiratory RSV positive specimens for week 2 2025, week 3 2025 and the 2024/2025 season. Data source: NVRL.

Time period

Specimen source

Total RSV positive

RSV A

RSV B

RSV (unspecified)

Week 2 2025

Sentinel GP ARI

21

13

8

0

Non-sentinel respiratory

67

21

46

0

Total

88

34

54

0

Week 3 2025

Sentinel GP ARI

10

2

8

0

Non-sentinel respiratory

38

11

26

1

Total

48

13

34

1

Season to date

Sentinel GP ARI

126

61

65

0

Non-sentinel respiratory

452

215

236

1

Total

578

276

301

1