ABSTRACT
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.
Subject(s)
COVID-19 , Cross Infection , Emergency Service, Hospital , COVID-19/epidemiology , COVID-19/transmission , Cross Infection/epidemiology , Cross Infection/virology , Genome, Viral , Humans , Ireland/epidemiology , Pandemics/prevention & control , Phylogeny , SARS-CoV-2/genetics , Whole Genome SequencingSubject(s)
COVID-19 , Pneumonia , Antibodies, Viral , Child , Humans , Ireland/epidemiology , SARS-CoV-2ABSTRACT
Presentation A 40-year-old healthcare worker (HCW) presented with cough, headache, sore throat, fatigue and myalgia seven months after primary infection with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms were milder and recovery was faster on the second episode. Diagnosis Reinfection with phylogenetically distinct SARS-CoV-2 was confirmed by whole-genome sequencing (WGS). Treatment Management involved symptomatic treatment and self-isolation. Discussion The incidence of SARS-CoV-2 reinfection is not well characterised. Infection control precautions may still be required in healthcare facilities, even in previously infected and possibly in vaccinated individuals while SARS-CoV-2 remains in circulation. Further research on the nature and duration of immunity is required to inform public health and infection control policy.