eLife (Sep 2022)

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

  • Oliver Stirrup,
  • James Blackstone,
  • Fiona Mapp,
  • Alyson MacNeil,
  • Monica Panca,
  • Alison Holmes,
  • Nicholas Machin,
  • Gee Yen Shin,
  • Tabitha Mahungu,
  • Kordo Saeed,
  • Tranprit Saluja,
  • Yusri Taha,
  • Nikunj Mahida,
  • Cassie Pope,
  • Anu Chawla,
  • Maria-Teresa Cutino-Moguel,
  • Asif Tamuri,
  • Rachel Williams,
  • Alistair Darby,
  • David L Robertson,
  • Flavia Flaviani,
  • Eleni Nastouli,
  • Samuel Robson,
  • Darren Smith,
  • Matthew Loose,
  • Kenneth Laing,
  • Irene Monahan,
  • Beatrix Kele,
  • Sam Haldenby,
  • Ryan George,
  • Matthew Bashton,
  • Adam A Witney,
  • Matthew Byott,
  • Francesc Coll,
  • Michael Chapman,
  • Sharon J Peacock,
  • COG-UK HOCI Investigators,
  • The COVID-19 Genomics UK (COG-UK) consortium,
  • Joseph Hughes,
  • Gaia Nebbia,
  • David G Partridge,
  • Matthew Parker,
  • James Richard Price,
  • Christine Peters,
  • Sunando Roy,
  • Luke B Snell,
  • Thushan I de Silva,
  • Emma Thomson,
  • Paul Flowers,
  • Andrew Copas,
  • Judith Breuer

DOI
https://doi.org/10.7554/eLife.78427
Journal volume & issue
Vol. 11

Abstract

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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.

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