Insights into the implementation of a whole genome sequencing report form (SRF) to reduce nosocomial SARS-CoV-2 within UK hospitals: a qualitative process evaluation using normalisation process theory (preprint)

Background Here we report on a process evaluation conducted as part of a large multisite non-randomised trial of the effectiveness of a whole genome sequence report form (SRF) to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours during the COVID − 19 pandemic. We detail how the SRF was implemented across a heterogeneous purposive sub-sample of hospital trial sites (n = 5/14). Methods We conducted in-depth interviews from diverse professional staff (N = 39). Inductive thematic analysis initially explored participants’ accounts of implementing the SRF. The resulting data driven themes, concerning the way the SRF was used within sites, were then coded in relation to the key tenets of normalisation process theory (NPT). Results Factors that enabled the implementation of the SRF included: elements of the context such as health care professional passion; the existence of whole genome sequencing (WGS) infrastructure; effective communication channels, the creation of new connections across professionals and teams; the integration of SRF-led discussions within pre-existing meetings and the ability of a site to achieve a rapid turnaround time. In contrast, we found factors that constrained the use of the SRF included elements of the context such as the impact of the Alpha-variant overwhelming hospitals. In turn, dealing with COVID-19 breached the limited capacity of infection prevention and control (IPC) to respond to the SRF and ensure its routinisation. Conclusion We show preliminary support for the SRF being an acceptable, useable and potentially scalable way of enhancing existing IPC activities. However, the context of both the trial and the alpha wave of COVID-19 limit these insights. Clinical trial number https://www.isrctn.com/ISRCTN50212645, Registration date 20/05/2020

Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study (preprint)

Introduction 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, 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 (IRR 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. 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.