CHARACTERSING WITHIN-HOSPITAL SARS-COV-2 TRANSMISSION EVENTS: A RETROSPECTIVE ANALYSIS INTEGRATING EPIDEMIOLOGICAL AND VIRAL GENOMIC DATA ACROSS TWO PANDEMIC WAVES. B.Lindsey1,2 , Ch.Julián Villabona-Arenas3,4 , F.Campbell5, A.Keeley1,2, M.Parker6,7,8, H.Parsons1,2 , P.Zhang1, N.Kakkar2 , M.Gallis1 , B.Foulkes1 , P.Wolverson1 , S.Louka1 , S.Christou1 , A.State2 , K.Johnson2 , M.Raza1,2, S.Hsu1,7 T.Jombart3,4,9, A.Cori9 , The COVID-19 Genomics UK consortium10, C.Evans1,2, D.Partridge1,2, K.Atkins3,4,11, S.Hué3,4 & T.Silva1,2 1. The Florey Institute for Host-Pathogen Interactions, University of Sheffield. 2. Sheffield Teaching Hospitals NHS Foundation Trust, 3. Centre for Mathematical Modelling of Infectious Diseases, LSHTM. 4. Department of Infectious Disease Epidemiology, LSHTM 5. Health Emergencies Programme, World Health Organization 6. Sheffield Biomedical Research Centre. 7. Sheffield Bioinformatics Core 8. The Department of Neuroscience/Neuroscience Institute, The 9. MRC Centre for Global Infectious Disease Analysis, Imperial College London. 10. https://www.cogconsortium.uk 11. Usher Institute, The University of Edinburgh

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in multiple hospital outbreaks, exposing healthcare workers and non COVID-19 patients to SARS-CoV-2 infection. To safely continue routine and elective activities in hospitals during times of high SARS-CoV-2 incidence, it is important to discern factors that drive hospital-acquired infections. This greater understanding can be used to protect staff and patients, as well as informing further efforts to contain hospital outbreaks.

A retrospective Bayesian modelling study was used to reconstruct transmission chains amongst 2181 patients and healthcare workers using combined viral genomic and epidemiological data at a large UK NHS Trust between 1st March 2020 and 25th July 2020 (Wave 1) and 30th November 2020 and 24th January 2021 (Wave 2).

Staff-to-staff transmission was estimated to be the most frequent transmission type during Wave 1. Patient-to-patient transmissions to become the predominant transmission type in Wave 2. Over 50% of hospital-acquired infections were concentrated in 8/120 locations in Wave 1 and 10/93 locations in Wave 2. Approximately 40% to 50% of hospital-onset patient cases resulted in onward transmission compared to less than 4% of definite community-acquired cases.

Prevention and control measures introduced during the COVID-19 pandemic may have had a significant impact on reducing infections between healthcare workers but were insufficient during the second wave to prevent a high number of patient-to-patient transmissions. As hospital-acquired cases appeared to drive most transmissions, more frequent and rapid identification and isolation of these cases will be required to break hospital transmission chains in subsequent pandemic waves.

Benjamin Lindsey, Sheffield Hospitals NHS Trust