TY - JOUR TI - Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study AU - Stirrup, Oliver AU - Blackstone, James AU - Mapp, Fiona AU - MacNeil, Alyson AU - Panca, Monica AU - Holmes, Alison AU - Machin, Nicholas AU - Shin, Gee Yen AU - Mahungu, Tabitha AU - Saeed, Kordo AU - Saluja, Tranprit AU - Taha, Yusri AU - Mahida, Nikunj AU - Pope, Cassie AU - Chawla, Anu AU - Cutino-Moguel, Maria-Teresa AU - Tamuri, Asif AU - Williams, Rachel AU - Darby, Alistair AU - Robertson, David L AU - Flaviani, Flavia AU - Nastouli, Eleni AU - Robson, Samuel AU - Smith, Darren AU - Loose, Matthew AU - Laing, Kenneth AU - Monahan, Irene AU - Kele, Beatrix AU - Haldenby, Sam AU - George, Ryan AU - Bashton, Matthew AU - Witney, Adam A AU - Byott, Matthew AU - Coll, Francesc AU - Chapman, Michael AU - Peacock, Sharon J AU - COG-UK HOCI Investigators AU - The COVID-19 Genomics UK (COG-UK) consortium AU - Hughes, Joseph AU - Nebbia, Gaia AU - Partridge, David G AU - Parker, Matthew AU - Price, James Richard AU - Peters, Christine AU - Roy, Sunando AU - Snell, Luke B AU - de Silva, Thushan I AU - Thomson, Emma AU - Flowers, Paul AU - Copas, Andrew AU - Breuer, Judith A2 - Bonten, Marc J A2 - van der Meer, Jos W A2 - Bonten, Marc J VL - 11 PY - 2022 DA - 2022/09/13 SP - e78427 C1 - eLife 2022;11:e78427 DO - 10.7554/eLife.78427 UR - https://doi.org/10.7554/eLife.78427 AB - 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. KW - COVID-19 KW - viral genomics KW - hospital-acquired infection KW - healthcare-associated infection KW - infection prevention KW - molecular epidemiology KW - infection control JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -