Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study

There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings. We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general transmission patterns according to case type (HCWs working in dedicated Covid-19 cohorting wards: HCW ; HCWs working in non-Covid-19 wards where outbreaks occurred: HCW ; patients with nosocomial Covid-19: patient ) by deriving the proportion of infections attributed to each case type across all posterior trees and comparing them to random expectations. During the study period (1 March to 7 May 2020), we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCW , 36 HCW ) and 53 patients. The attack rates ranged from 10% to 19% for patients, and 21% for HCWs. We estimated that 16 importation events occurred with high confidence (4 patients, 12 HCWs) that jointly led to up to 41 secondary cases; in six additional cases (5 HCWs, 1 patient), importation was possible with a posterior probability between 10% and 50%. Most patient-to-patient transmission events involved patients having shared a ward (95.2%, 95% credible interval [CrI] 84.2%-100%), in contrast to those having shared a room (19.7%, 95% CrI 6.7%-33.3%). Transmission events tended to cluster by case type: patient were almost twice as likely to be infected by other patient than expected (observed:expected ratio 2.16, 95% CrI 1.17-4.20, p=0.006); similarly, HCW were more than twice as likely to be infected by other HCW than expected (2.72, 95% CrI 0.87-9.00, p=0.06). The proportion of infectors being HCW was as expected as random. We found a trend towards a greater proportion of high transmitters (≥2 secondary cases) among HCW than patient in the late phases (28.6% vs. 11.8%) of the outbreak, although this was not statistically significant. Most importation events were linked to HCW. Unexpec