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UK Study Considers Rapid, Slower SARS-CoV-2 Sequencing Strategies for Infection Control in Hospitals

In eLife, a University College London-led team presents findings from a prospective, non-randomized trial done in the winter of 2020 and 2021 that looked at SARS-CoV-2 sequencing as an infection prevention control (IPC) measure in more than a dozen acute UK National Health Service hospital trusts. With data generated at the COVID-19 Genomics UK sequencing hub together with a tailored reporting strategy, the researchers compared eight weeks of rapid viral sequencing to four weeks of SARS-CoV-2 sequencing with a five-to-10-day turnaround. From 2,170 "hospital-onset COVID-19 infections" (HOCIs) reported from October 2020 to April 2021, they produced SARS-CoV-2 sequences for 650 cases during the study's intervention phase. Although the rapid and non-rapid SARS-CoV-2 sequencing approaches led to IPC changes in a significant subset of the cases, the approach did not seem to significantly alter transmission during the time period considered. "While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within five days," they report, noting that "substantial difficulties were encountered in implementing the intervention and in responding effectively to any insights generated."