Reconstructing transmission chains of SARS-CoV-2 amid multiple outbreaks in a geriatric acute-care hospital (preprint)

ABSTRACT

Background 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. Methods 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, in order to determine who infected whom. We evaluated general transmission patterns according to type of case (HCWs working in dedicated Covid-19 cohorting wards HCWcovid; HCWs working in non-Covid-19 wards where outbreaks occurred HCWoutbreak; patients with nosocomial Covid-19 patientnoso) by deriving the proportion of infections attributed to each type of case across all posterior trees and comparing them to random expectations. Results During the study period (March 1 to May 7, 2020) we included 180 SARS-CoV-2 positive cases 127 HCWs (91 HCWcovid, 36 HCWoutbreak) and 53 patients. The attack rates ranged from 10-19% for patients, and 21% for HCWs. We estimated that there were 16 importation events (3 patients, 13 HCWs) that jointly led to 16 secondary cases. Most patient-to-patient transmission events involved patients having shared a ward (97.6%, 95% credible interval [CrI] 90.4-100%), in contrast to those having shared a room (44.4%, 95%CrI 27.8-62.5%). Transmission events tended to cluster by type of case patientnoso were almost twice as likely to be infected by other patientnoso than expected (observedexpected ratio 1.91, 95%CrI 1.08 - 4.00, p = 0.02); similarly, HCWoutbreak were more than twice as likely to be infected by other HCWoutbreak than expected (2.25, 95%CrI 1.00-8.00, p = 0.04). The proportion of infectors of HCWcovid were as expected as random. The proportions of high transmitters ([≥]2 secondary cases) were significantly higher among HCWoutbreak than patientnoso in the late phases (26.2% vs. 13.4%, p<2.2e-16) of the outbreak. Conclusions Most importation events were linked to HCW. Unexpectedly, transmission between HCWcovid was more limited than transmission between patients and HCWoutbreak. This highlights gaps in infection control and suggests possible areas of improvements to limit the extent of nosocomial transmission.