COVID-19 incidence and outcome by affluence/deprivation across three pandemic waves in Ireland: A retrospective cohort study using routinely collected data.

BACKGROUND: Since the pandemic onset, deprivation has been seen as a significant determinant of COVID-19 incidence and mortality. This study explores outcomes of COVID-19 in the context of material deprivation across three pandemic waves in Ireland. METHODS: Between 1st March 2020 and 13th May 2021, 252,637 PCR-confirmed COVID-19 cases were notified in Ireland. Cases were notified to the national Computerised Infectious Disease Reporting (CIDR) system. Each case was geo-referenced and assigned a deprivation category according to the Haase-Pratschke (HP) Deprivation Index. Regression modelling examined three outcomes: admission to hospital; admission to an intensive care unit (ICU) and death. RESULTS: Deprivation increased the likelihood of contracting COVID-19 in all age groups and across all pandemic waves, except for the 20-39 age group. Deprivation, age, comorbidity and male gender carried increased risk of hospital admission. Deprivation was not a factor in predicting ICU admission or death, and diagnosis in wave 2 was associated with the lowest risk of all three outcomes. CONCLUSIONS: Our study suggests that COVID-19 spreads easily through all strata of society and particularly in the more deprived population; however this was not a consistent finding. Ireland is ethnically more homogenous than other countries reporting a larger deprivation gradient, and in such societies, structural racial differences may contribute more to poor COVID outcomes than elements of deprivation.

Compliance with local travel restrictions and face masks during first phase of COVID-19 pandemic in Ireland: a national survey.

BACKGROUND: This study examines compliance with local travel restrictions and assesses early uptake of mask wearing, during the initial phase of the coronavirus disease of 2019 (COVID-19) pandemic in Ireland, to inform the ongoing outbreak response. METHODS: A series of four nationally representative telephone surveys were developed. Information was collected at a household level and from primary respondents. Multivariable logistic regression estimated the association between sociodemographic characteristics and compliance with the local travel restriction and with mask use in primary respondents. RESULTS: Household compliance with local travel restrictions was similar by region, household size and social position. 73.4% of all household members complied, with high levels maintained over time. Higher proportions reported travelling for non-permitted reasons with time. Older age, female gender and attending higher education were independently associated with compliance to local travel restrictions. Among primary respondents, no factors were independently associated with mask use. CONCLUSION: High compliance with local travel restrictions during the early stages of the pandemic demonstrates the engagement of the population with public health guidance. Although high compliance with local travel restrictions was generally maintained over time, non-permitted activities increased. Early adoption of mask use before required by national policy or legislation provides further evidence of the responsiveness of the population.

Age-specific associations between underlying health conditions and hospitalisation, death and in-hospital death among confirmed COVID-19 cases: a multi-country study based on surveillance data, June to December 2020.

BackgroundUnderlying conditions are risk factors for severe COVID-19 outcomes but evidence is limited about how risks differ with age.AimWe sought to estimate age-specific associations between underlying conditions and hospitalisation, death and in-hospital death among COVID-19 cases.MethodsWe analysed case-based COVID-19 data submitted to The European Surveillance System between 2 June and 13 December 2020 by nine European countries. Eleven underlying conditions among cases with only one condition and the number of underlying conditions among multimorbid cases were used as exposures. Adjusted odds ratios (aOR) were estimated using 39 different age-adjusted and age-interaction multivariable logistic regression models, with marginal means from the latter used to estimate probabilities of severe outcome for each condition-age group combination.ResultsCancer, cardiac disorder, diabetes, immunodeficiency, kidney, liver and lung disease, neurological disorders and obesity were associated with elevated risk (aOR: 1.5-5.6) of hospitalisation and death, after controlling for age, sex, reporting period and country. As age increased, age-specific aOR were lower and predicted probabilities higher. However, for some conditions, predicted probabilities were at least as high in younger individuals with the condition as in older cases without it. In multimorbid patients, the aOR for severe disease increased with number of conditions for all outcomes and in all age groups.ConclusionWhile supporting age-based vaccine roll-out, our findings could inform a more nuanced, age- and condition-specific approach to vaccine prioritisation. This is relevant as countries consider vaccination of younger people, boosters and dosing intervals in response to vaccine escape variants.

Establishing a COVID-19 pandemic severity assessment surveillance system in Ireland.

We developed a COVID-19 pandemic severity assessment (PSA) monitoring system in Ireland, in order to inform and improve public health preparedness, response and recovery. The system based on the World Health Organization (WHO) Pandemic Influenza Severity Assessment (PISA) project included a panel of surveillance parameters for the following indicators: transmissibility, impact and disease severity. Age-specific thresholds were established for each parameter and data visualised using heat maps. The findings from the first pandemic wave in Ireland have shown that the WHO PISA system can be adapted for COVID-19, providing a standardised tool for early warning and monitoring pandemic severity.

Increasing risk of breakthrough COVID-19 in outbreaks with high attack rates in European long-term care facilities, July to October 2021.

We collected data from 10 EU/EEA countries on 240 COVID-19 outbreaks occurring from July-October 2021 in long-term care facilities with high vaccination coverage. Among 17,268 residents, 3,832 (22.2%) COVID-19 cases were reported. Median attack rate was 18.9% (country range: 2.8-52.4%), 17.4% of cases were hospitalised, 10.2% died. In fully vaccinated residents, adjusted relative risk for COVID-19 increased with outbreak attack rate. Findings highlight the importance of early outbreak detection and rapid containment through effective infection prevention and control measures.

Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021.

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).

Underlying conditions and risk of hospitalisation, ICU admission and mortality among those with COVID-19 in Ireland: A national surveillance study.

BACKGROUND: To date, over 2 million people worldwide have died with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To describe the experience in Ireland, this study examined associations between underlying conditions and the following outcomes: mortality, admission to hospital or admission to the intensive care unit (ICU) among those infected with COVID-19. METHODS: This study used data from the Health Protection Surveillance Centre in Ireland and included confirmed cases of COVID-19 from the first wave of the pandemic between March and July 2020. Two cohorts were included: all cases (community and hospital) and hospital admissions only. For all cases, health outcome data included mortality and hospitalisation. For hospitalised cases, outcome data included mortality and ICU admission. Logistic regression was used to examine associations between underlying conditions and outcomes across both cohorts. Results are presented as adjusted odds ratios (OR) and 95% confidence intervals (CIs). FINDINGS: There were 19,789 cases included in analysis, which encompassed 1,476 (7.5%) deaths, 2,811 (14.2%) hospitalisations, and 438 (2.2%) ICU admissions of whom 90 (20.5%) died. Significantly higher risk of mortality, hospitalisation and ICU admission was associated with having chronic heart disease, a BMI ≥40kg/m2 and male sex. Additionally, diagnosis of a chronic neurological condition (OR 1.41; 95%CI:1.17, 1.69), chronic kidney disease (OR 1.74; 95%CI:1.35, 2.24) and cancer (OR 2.77; 95%CI:2.21, 3.47) were significantly associated with higher risk of mortality among all cases, with similar patterns of association observed for mortality among hospitalised cases. INTERPRETATION: The identification of underlying conditions among COVID-19 cases may help identify those at highest risk of the worst health outcomes and inform preventive strategies to improve outcomes. FUNDING: This study was supported by the Health Service Executive, Health Protection Surveillance Centre. KEB and MM are funded by the Health Research Board (RL-15-1579 and EIA-2019-012 respectively).

Epidemiology of COVID-19 and public health restrictions during the first wave of the pandemic in Ireland in 2020.

BACKGROUND: We describe the epidemiological trends and report and review the public health restrictions implemented during the first wave of the COVID-19 pandemic in Ireland. METHODS: The study reviewed confirmed cases of COVID-19 notified from 1 March to 18 July 2020. Data were obtained from the national COVID-19 Data Hub, the National Health Protection Surveillance Centre, the National Contact Management Programme and the European Centre for Disease Prevention and Control. RESULTS: A total of 25 617 cases were notified during the study period. Weekly cases and deaths peaked in mid-April 2020 at 5701 and 316, respectively. Mean number of close contacts per case was lowest at 0.7 in April, rising to 6.6 by July. Outbreak settings shifted from travel and workplace in March, to healthcare in April. Restrictions implemented on 12 March extended to full lockdown on 27 March. Phased relaxation of restrictions commenced 18 May. Effective suppression of community transmission of COVID-19 was achieved by June 2020. CONCLUSION: Lockdown is a crude population-level restriction effective in controlling COVID-19. Phased relaxation of restrictions in Ireland, however, led to an immediate increase in mean number of contacts per case, which facilitates viral transmission unless individual-level restrictions are adhered to. This demonstrates a limitation of lockdown as a long-term mechanism of pandemic control.

A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020.

An outbreak of 59 cases of coronavirus disease (COVID-19) originated with 13 cases linked by a 7 h, 17% occupancy flight into Ireland, summer 2020. The flight-associated attack rate was 9.8-17.8%. Spread to 46 non-flight cases occurred country-wide. Asymptomatic/pre-symptomatic transmission in-flight from a point source is implicated by 99% homology across the virus genome in five cases travelling from three different continents. Restriction of movement on arrival and robust contact tracing can limit propagation post-flight.

Covid-19 Estimating the burden of symptomatic disease in the community and the impact of public health measures on physical, mental and social wellbeing: a study protocol.

Introduction: Covid-19 was declared a pandemic in March 2020. Since then, governments have implemented unprecedented public health measures to contain the virus. This study will provide evidence to inform responses to the pandemic by: i) estimating population prevalence and trends of self-reported symptoms of Covid-19 and the proportions of symptomatic individuals and household contacts testing positive for Covid-19; ii) describing acceptance and compliance with physical-distancing measures, explore effects of public health measures on physical, mental and social wellbeing; iii) developing a mathematical network model to inform decisions on the optimal levels of physical distancing measures. Methods: Two cross-sectional nationally-representative telephone surveys will be conducted in Ireland using random digit-dialling, with response rates estimates based on proportion of non-operational and non-answering numbers. The first survey with four waves in May and June will address adherence to social distancing measures and whether the respondent or other household members are or have been unwell during the preceding two weeks with one or more symptoms of Covid-19. The second survey with three waves in June, July and September will address knowledge, attitudes, and compliance towards physical-distancing measures and physical, mental and social wellbeing. The mathematical network model will be developed for all-Ireland (on various levels of spatial granularity including the scale of counties and electoral divisions) based on outputs from both cross-sectional surveys and relevant publicly available data to inform decisions on optimal levels and duration of physical distancing measures. Discussion: This study will contribute to our understanding of the impact and sustainability of public health measures of the Covid-19 pandemic. Findings will have long-lasting benefits, informing decision-making on the best levels, and duration of physical-distancing measures, balancing a range of factors including capacity of the health service with the effects on individuals' wellbeing and economic disruption. Findings will be shared with key policy-makers.

Use of anti-reflux medications in infants under 1 year of age: a retrospective drug utilization study using national prescription reimbursement data.

Non-specific symptoms such as irritability, vomiting, and back arching during the infant period are often attributed to gastroesophageal reflux. While numerous studies have shown no significant benefit to the use of acid suppressant medications in this population, these medications are frequently prescribed in response to these symptoms. Our goals were to understand how often children were being prescribed this medication. To do this, data was extracted from a national database for reimbursement of prescribed medications through the General Medical Services scheme (GMS). Infants aged less than 1 year and eligible for reimbursement under GMS were included for analysis. A total of 450 infants per 10,000 eligible population received an anti-reflux preparation from the following drug classes (H2 antagonists, proton pump inhibitors, or alginate preparations) in 2018. This is compared with that in 2009 where only 137 per 10,000 eligible infants received these medications. This increase was predominantly attributable to an increase in ranitidine prescriptions.Conclusion: Despite a change in clinical guidelines, anti-reflux preparations are increasingly being prescribed to infants aged less than 1 year. The reasons behind the increase in prescriptions containing these medications cannot be ascertained from this data. This may suggest a proportion of these prescriptions may be unwarranted in this population. What is Known: • The prescription of PPIs in infants has increased in a number of countries. • Use of anti-reflux medications has a very poor evidence base in infancy. What is New: • This data focuses only on an infant age group in a "well" cohort. • Ranitidine may contribute to increased acid-suppressant use in infancy.

Epidemiology of Campylobacter infections in Ireland 2004-2016: What has changed?

Campylobacter is the most common notifiable cause of bacterial gastroenteritis in humans in Ireland. However, epidemiological information is limited. We aimed to describe Campylobacter epidemiology in Ireland and trends over time, to inform future surveillance and research. We reviewed data completeness and described notified cases of campylobacteriosis (2004-2016) by age, sex, geographical area, season and trends over time. We used negative binomial regression to estimate incidence rate ratios (IRR) and adjusted IRR (aIRR) by age group, sex, geographical area and season. We undertook interrupted time-series analysis by age group and geographical area incorporating terms for trend and period (2004-2010 and 2011-2016). There were 27,034 cases of campylobacteriosis notified between 2004 and 2016. Data were >99% complete for notification date, geographical area, sex and date of birth. Crude annual incidence ranged from 36.2 to 54.4 per 100,000 population. The incidence was higher in, males (aIRR 1.15, 95% confidence intervals (CI) 1.12-1.19), those aged <5 years compared with the lowest incidence age group (45-64 years) (aIRR 4.65, 95% CI 4.43-4.88), other seasons compared with winter and all other areas compared with the north-east area (aIRR range 1.22-1.71, p-values <.001). In 2011, we observed a stepped increase in annual crude incidence overall, in both sexes, all age groups and most geographical areas. This pattern was mirrored on time-series analysis, with significant increases in trend-adjusted incidences of 30%-45% (p-values ≤.008) detected for all age groups and 30%-66% (p-values ≤.012) for seven out of eight geographical areas after 2011. Campylobacter remains the most commonly notified bacterial cause of gastroenteritis in Ireland. With available information, we could not fully explain a stepped increase in incidence observed in 2011. The transition of regional laboratories from culture-based to molecular-based Campylobacter diagnostic methods was a possible contributor. However, further investigation is required to fully explain the identified changes.

Use of geosocial networking applications is independently associated with diagnosis of STI among men who have sex with men testing for STIs: findings from the cross-sectional MSM Internet Survey Ireland (MISI) 2015.

OBJECTIVES: MSM Internet Survey Ireland (MISI) 2015 was an anonymous, self-completed, cross-sectional internet survey assessing sexual behaviours and health needs among men who have sex with men (MSM) in Ireland. We explored factors associated with self-reported STI diagnosis among MSM who were sexually active and had an STI test in the previous year. METHODS: We compared the study population (n=1158; 37% of total population), with the sexually active MISI population not testing for STIs (n=1620; 52% of total population). Within the study population, we identified sociodemographics and sexual behaviours associated with self-reporting STI diagnosis. We used multivariable logistic regression to estimate adjusted odds ratios (aORs). RESULTS: The sociodemographics, lifestyle and sexual behaviours of the study population differed significantly from the sexually active MISI population who did not test for STIs. Within the study population, 65% met a sexual partner via geosocial networking smartphone application (GSNa) and 21% self-reported an STI diagnosis in the previous year. On univariable analysis, factors associated with STI diagnosis included: older age, identifying as gay, HIV-positive status, increasing number of sexual partners in the previous year, condomless anal intercourse (CAI) with ≥2 non-steady partners and using GSNa to meet a new sexual partner in the previous year or most recent sexual partner. On multivariable analysis, STI diagnosis was associated with: being aged 25-39 years (aOR 1.8, 95% CI 1.04 to 3.15), CAI with ≥2 non-steady partners (aOR 2.8, 95% CI 1.84 to 4.34), total number of sexual partners (aOR 1.02, 95% CI 1.00 to 1.03) and using GSNa to meet a new sexual partner (aOR 1.95, 95% CI 1.12 to 3.39). CONCLUSIONS: STI diagnosis among MSM testing for STIs is associated with GSNa use, as well as sexual behaviours. GSNas are key settings for STI prevention interventions, which should prioritise men with high numbers of sexual partners and those with multiple CAI partners.

Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer.

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates.