Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves

<jats:title>Structured abstract</jats:title><jats:sec><jats:title>Objectives</jats:title><jats:p>To characterise within-hospital SARS-CoV-2 transmission across two waves of the COVID-19 pandemic.</jats:p></jats:sec><jats:sec><jats:title>Design</jats:title><jats:p>A retrospective Bayesian modelling study to reconstruct transmission chains amongst 2181 patients and healthcare workers using combined viral genomic and epidemiological data.</jats:p></jats:sec><jats:sec><jats:title>Setting</jats:title><jats:p>A large UK NHS Trust with over 1400 beds and employing approximately 17,000 staff.</jats:p></jats:sec><jats:sec><jats:title>Participants</jats:title><jats:p>780 patients and 522 staff testing SARS-CoV-2 positive between 1st March 2020 and 25th July 2020 (Wave 1); and 580 patients and 299 staff testing SARS-CoV-2 positive between 30th November 2020 and 24th January 2021 (Wave 2).</jats:p></jats:sec><jats:sec><jats:title>Main outcome measures</jats:title><jats:p>Transmission pairs including who-infected-whom; location of transmission events in hospital; number of secondary cases from each individual, including differences in onward transmission from community and hospital onset patient cases.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Staff-to-staff transmission was estimated to be the most frequent transmission type during Wave 1 (31.6% of observed hospital-acquired infections; 95% CI 26.9 to 35.8%), decreasing to 12.9% (95% CI 9.5 to 15.9%) in Wave 2. Patient-to-patient transmissions increased from 27.1% in Wave 1 (95% CI 23.3 to 31.4%) to 52.1% (95% CI 48.0 to 57.1%) in Wave 2, to become the predominant transmission type. 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.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Prevention and control measures that evolved 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 onward transmissions, more frequent and rapid identification and isolation of these cases will be required to break hospital transmission chains in subsequent pandemic waves.</jats:p></jats:sec>