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medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.02.10.22270799


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.

ssrn; 2020.
Preprint in English | PREPRINT-SSRN | ID: ppzbmed-10.2139.ssrn.3734290


Background: Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. Infection control is challenging in these environments due to regular contact between healthcare workers (HCWs) and patients. This is amplified by increased frequency of severe adverse responses to SARS-CoV-2 in patients with underlying health conditions. Methods: We sequenced SARS-CoV-2 genomes for patients and HCWs across multiple geographically distinct UK hospitals. All hospitals were actively enforcing zoning approaches (SARS-CoV-2 negative and SARS-CoV-2 positive areas) as an infection control measure. We integrated patient movement and staff location data into the analysis of viral genome data in order to understand geographical and temporal dynamics of SARS-CoV-2 transmission. Findings: We obtained 173 high-quality SARS-CoV-2 genomes from patients ( n =134) and HCWs ( n =39). The median number of genomic variants per sample of 11 (range=0-16), with a 61.5% average pairwise similarity in the variants (range=0-100%). Integration of patient movement identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples ( p <0.001). Incorporation of HCW location further increased the number of individuals within PCCs. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location ( p <0.001). Interpretation: SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters and improved understanding of the role of patient-HCW interactions. This dynamic approach to SARS-CoV-2 outbreak monitoring in a healthcare setting is able to support infection control management strategies within the healthcare setting. Funding: JME is funded by a postdoctoral research fellowship from Health Education England. WGN is supported by the Manchester NIHR BRC (IS-BRC-1215-20007).Declaration of Interests: The authors declare no conflicts of interest.Ethics Approval Statement: The study was conducted to investigate hospital outbreak investigation/surveillance. Ethical approval was obtained from the Manchester Biomedical Research Centre COVID-19 rapid response group for viral genome analysis.

Cross Infection , COVID-19