Table 1. Case numbers in the five major ward clusters.

‘Total cases before network analysis’ were derived by adding patients with potential hospital-acquired COVID-19 infections and HCW cases from each ward. The five wards with the largest combined number of HAI and HCW cases within the study period were analysed, with anonymised ward names A to E. ‘Ward type’ refers to whether wards were ‘green’ (intended for patients negative for COVID-19), or ‘red’ (intended for COVID-19 patients). The breakdown of HAI and HCW cases for each of the included wards is shown in columns ‘HAI cases before network analysis’ and ‘HCW cases before network analysis’, respectively. The ‘network analysis’ at this stage identified additional patients that could have been involved in transmission with the HAI patients on the basis of co-location on the same or other wards within a plausible timeframe for SARS-CoV-2 transmission (described in Materials and methods). This yielded the final cases analysed for each ward cluster using the transmission reconstruction model. The final column shows the number of cases from each ward cluster for which genomic data were available. In total, there were 98 cases with genomic data and 129 SARS-CoV-2 genomes analysed in the study (the larger number of genomes than cases is because of multiple samples per patient that underwent SARS-CoV-2 sequencing). Three patients were included in two ward clusters each (which is why the total of the ‘Cases after network analysis with genomic data’ column is 101). HAI = hospital-acquired infection (definition in Methods); HCW = healthcare worker.

Ward name	Ward type	Total cases before network analysis	HAI cases before network analysis	HCW cases before network analysis	Cases after network analysis	Cases after network analysis with genomic data
A	Green	14	12	2	16	15
B	Green	11	2	9	15	12
C	Green	12	5	7	20	19
D	Green	14	4	10	16	16
E	Red	13	3	10	47	39