Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.

AIM: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.

Low prevalence of SARS-CoV-2 detected in symptomatic children admitted to hospital

Aims Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in 2019 and is responsible for the condition known as COVID-19. COVID-19 was first reported in Ireland in February 2020 with University Hospital Limerick’s (UHL) first paediatric case reported on 4th March 2020. Studies have shown clinical manifestations of children’s cases are generally less severe than those of adults. UHL serves a catchment population of approximately 100,000 children. We aimed to describe the clinical presentation, and prevalence of SARS-CoV-2, in children requiring inpatient hospitalization during the initial phase of the pandemic in Ireland. Methods Data were examined relating to all inpatients aged 0 – 16 years admitted with a queried or confirmed diagnosis of COVID-19 from 8th February 2020 to 8th June 2020. Emergency Department notes and inpatient records along with laboratory and radiology records were reviewed. Results 220 paediatric inpatients were tested by PCR for SARS-CoV-2 during this period;101 (45.9%) were female. Ninety-five (43.2%) were diagnosed with ‘viral illnesses’. Seven (3.2%) had laboratory-confirmed SARS-CoV-2, with an average age of 8.1 years (range: 0.59 years to 13.77 years). There were two Kawasaki-like illnesses admitted;both tested negative for SARS-CoV-2 on PCR. In our SARS-CoV-2 positive cohort, there was no associated significant morbidity and no associated mortality. Conclusion During the initial phase of the COVID-19 pandemic, prevalence of confirmed SARS-CoV-2 in symptomatic hospitalised children was low at 3.2%.