Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study

Oliver Stirrup, James Blackstone, Fiona Mapp, Alyson Macneil, Monica Panca, Alison Holmes, Nicholas Machin, Gee Yee Shin, Tabitha W Mahungu, Kordo Saeed, Tranprit Saluja, Yusri Taha, Nikunj Mahida, Cassie F Pope, Anu Chawla, Maria-Teresa Cutino-Moguel, Asif Tamuri, Rachel Williams, Alistair Darby, David L RobertsonFlavia Flaviani, Eleni Nastouli, Samuel Robson, Darren Smith, Kenneth Laing, Irene Monahan, Beatrix Kele, Sam Haldenby, Ryan George, Matthew Bashton, Adam A Witney, Matthew Byott, Francesc Coll, Michael Chapman, Sharon J Peacock, Joseph Hughes, Gaia Nebbia, David G Partridge, Matthew Parker, James Richard Price, Christine Peters, Sunando Roy, Luke Blagdon Snell, Thushan I de Silva, Emma C Thomson, Paul Flowers, Andrew Copas, Judith Breuer

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected ≥48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. Results: A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. Conclusions: 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 5 days. Funding: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. Clinical trial number: NCT04405934.

Original languageEnglish
Article numbere78427
Publication statusPublished - 13 Sept 2022


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