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' (<48h) and 4 weeks of 'longer-turnaround' (5-10 day) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital onset COVID-19 infections (HOCIs; detected ≥48h from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on incidence of probable/definite hospital-acquired infections (HAIs) was evaluated.
Results: A total of 2170 HOCI cases were recorded from October 2020-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.
Conclusion: 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.
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Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G., Mahungu, T., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C., Chawla, A., Cutino-Moguel, M., Tamuri, A., Williams, R., Darby, A., Robertson, D., Flaviani, F., Nastouli, E., Robson, S., Smith, D., Laing, K., Monahan, I., Kele, B., Haldenby, S., George, R., Bashton, M., Witney, A., Byott, M., Coll, F., Chapman, M., Peacock, S., Hughes, J., Nebbia, G., Partridge, D., Parker, M., Price, J., Peters, C., Roy, S., Snell, L., de Silva, T., Thomson, E., Flowers, P., Copas, A. & Breuer, J. 2022, 'Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study', eLife, 11, article no: e78427. https://doi.org/10.7554/elife.78427