The authors were interested in how rapid SARS-CoV-2 sequencing can be combined with detailed epidemiological analysis to investigate healthcare associated infections and inform infection control measures. They conducted a prospective surveillance study using rapid SARS-CoV-2 nanopore sequencing from PCR-positive diagnostic samples from hospitals, enabling sample-to-sequence in less than 24 hours. Between March and April samples were collected from 5613 patients with COVID-19 from across the East of England. 1000 samples were sequenced, producing 747 high-quality genomes. These were combined with the epidemiological data of 299 patients from a single hospital, identifying 35 clusters of identical viruses involving 159 patients. 58% of 159 patients had strong epidemiological links and 20% had plausible epidemiological links. These results were then fed back to clinical, infection control and hospital management teams, leading to infection-control interventions and informed patient safety reporting. Therefore real-time genomic surveillance of SARS-CoV-2 can be conducted in a UK hospital, allowing for the investigation of healthcare associated COVID-19.
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