SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance.

SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.

Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021.

We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.

Fetal Deaths in Ireland Due to SARS-CoV-2 Placentitis Caused by SARS-CoV-2 Alpha.

CONTEXT.­: A severe third wave of COVID-19 disease affected Ireland in the first 3 months of 2021. In this wave, 1 second-trimester miscarriage and 6 stillbirths were observed in the Irish population because of placental insufficiency as a result of SARS-CoV-2 placentitis. This observation was at odds with the country's previous experience with COVID-19 disease in pregnant mothers. OBJECTIVE.­: To describe the clinical and pathologic features of these pregnancy losses. DESIGN.­: Retrospective review of clinical and pathologic data of cases of second-trimester miscarriage, stillbirth, or neonatal death identified by perinatal pathologists as being due to SARS-CoV-2 placentitis during the third wave of COVID-19 in Ireland. RESULTS.­: Clinical and pathologic data were available for review in 6 pregnancies. Sequencing or genotyping of the virus identified SARS-CoV-2 alpha (B.1.1.7) in all cases. Three of the 6 cases had maternal thrombocytopenia, and fetal growth restriction was not prominent, suggesting a rapidly progressive placental disease. CONCLUSIONS.­: The identification of SARS-CoV-2 alpha in all these cases suggests that the emergence of the variant was associated with an increased risk of fetal death due to SARS-CoV-2 placentitis when compared with the original virus. Maternal thrombocytopenia may have potential as a clinical marker of placentitis, but other inflammatory markers need investigation. Three of the 6 women had been assessed for reduced fetal movements in hospital some days before the fetal deaths actually occurred; this could suggest that there may be a window for intervention in some cases.

Transmission of SARS-CoV-2 arising from international flights arriving in Ireland in December 2020: a descriptive analysis using national surveillance data.

OBJECTIVES: There is limited evidence on the risk of in-flight transmission of SARS-CoV-2. This study estimated the extent of in-flight SARS-CoV-2 transmission on international flights arriving in Ireland during December 2020. STUDY DESIGN: This was a cross-sectional analysis. METHODS: National surveillance data identified all notified cases of COVID-19 who were infectious while travelling on international flights to Ireland during December 2020. Close contacts of cases were tested for SARS-CoV-2, and the results were collated to estimate the pooled secondary attack rate across all flights. Laboratory and epidemiological data were obtained from the Health Service Executive Covid Care Tracker, a national database of COVID-19 cases in Ireland. RESULTS: A total of 165 infectious cases of COVID-19 were identified on 134 incoming flights; 40.0% were symptomatic on board. There were 2099 flight close contacts identified, of whom 40.9% had results of a SARS-CoV-2 polymerase chain reaction test within 14 days of arrival. The pooled secondary attack rate for these contacts was 7.0% and was higher among those on flights of ≥5-hour duration (P = 0.008). More than half (59.1%) of close contacts had no SARS-CoV-2 test result recorded; the reasons included incorrect or absent contact details (26.5%) and no response when contacted (17.8%). CONCLUSIONS: In this national study investigating transmission of SARS-CoV-2 from international flights arriving into Ireland, the pooled secondary attack rate was 7.0%. International travel is likely to have contributed to the third wave of SARS-CoV-2 infections in Ireland in early 2021. Application of non-pharmaceutical interventions remains central to mitigating the risk of in-flight transmission.

Treating COVID-19 in the nursing home setting: an integrated approach for a complex and susceptible cohort.

Our patient, a nursing home resident, was reviewed by our frailty outreach service in November 2020. She initially was diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in September 2020 during an outbreak in her nursing home. On this occasion, she again tested positive for SARS-CoV-2. Our case report describes the resident's poor immune response indicated by a low IgG level after her initial COVID infection as well as reinfection with a 'non-variant' SARS-CoV-2 lineage (B.1.177). The case describes the importance of integration of community and secondary care. The nursing home received close monitoring and nurse supervision for the detection of potential deterioration of the patient. Exit-seeking behaviour by nursing home residents was limited effectively. The issues of low immune response to COVID-19 in older people and the emergence of variants of concern will continue to pose a threat to this susceptible group.

Genomic epidemiological analysis of SARS-CoV-2 household transmission.

Family clusters have contributed significantly to the onward spread of SARS-CoV-2. However, the dynamics of viral transmission in this setting remain incompletely understood. We describe the clinical and viral-phylogenetic characteristics of a family cluster of SARS-CoV-2 infections with a high attack rate, and explore how whole-genome sequencing (WGS) can inform outbreak investigations in this context. In this cluster, the first symptomatic case was a 22-month-old infant who developed rhinorrhoea and sneezing 2 days prior to attending a family gathering. Subsequently, seven family members in attendance at this event were diagnosed with SARS-CoV-2 infections, including the infant described. WGS revealed indistinguishable SARS-CoV-2 genomes recovered from the adults at the gathering, which were closely related genetically to B.1 lineage viruses circulating in the local community. However, a divergent viral sub-lineage was recovered from the infant and another child, each harbouring a distinguishing spike substitution (N30S). This suggested that the infant was unlikely to be the primary case, despite displaying symptoms first, and additional analysis of her nasopharyngeal swab revealed a picornavirus co-infection to account for her early symptoms. Our findings demonstrate how WGS can elucidate the transmission dynamics of SARS-CoV-2 infections within household clusters and provide useful information to support outbreak investigations. Additionally, our description of SARS-CoV-2 viral lineages and notable variants circulating in Ireland to date provides an important genomic-epidemiological baseline in the context of vaccine introduction.