Nosocomial Outbreak of SARS-CoV-2 in a “Non-COVID-19” Hospital Ward: Virus Genome Sequencing as a Key Tool to Understand Cryptic Transmission

Abstract

Dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions affects both patients and health-care workers (HCW), as well as the institutional capacity to provide essential health services. Here, we investigated an outbreak of SARS-CoV-2 in a “non-COVID-19” hospital ward unveiled by massive testing, which challenged the reconstruction of transmission chains. The contacts network during the 15-day period before the screening was investigated, and positive SARS-CoV-2 RNA samples were subjected to virus genome sequencing. Of the 245 tested individuals, 48 (21 patients and 27 HCWs) tested positive for SARS-CoV-2. HCWs were mostly asymptomatic, but the mortality among patients reached 57.1% (12/21). Phylogenetic reconstruction revealed that all cases were part of the same transmission chain. By combining contact tracing and genomic data, including analysis of emerging minor variants, we unveiled a scenario of silent SARS-CoV-2 dissemination, mostly driven by the close contact within the HCWs group and between HCWs and patients. This investigation triggered enhanced prevention and control measures, leading to more timely detection and containment of novel outbreaks. This study shows the benefit of combining genomic and epidemiological data for disclosing complex nosocomial outbreaks, and provides valuable data to prevent transmission of COVID-19 in healthcare facilities.

Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

“…Secondly, at least 33% of SARS-CoV-2 infections in adults are thought to be asymptomatic 5 , therefore identifying all patients and HCWs contributing to transmission is challenging. In the limited instances where viral genomic data were analysed, this information was used to confirm or complement a purely epidemiological approach 6 – 9 . Elucidating the source of transmission events on the basis of viral genetic relatedness alone also entails considerable uncertainty due to the slow evolutionary rate of SARS-CoV-2 10 .…”

Enhancing epidemiological investigation of nosocomial SARS-CoV-2 infection with whole genome sequencing: A retrospective cohort study across four hospitals in the UK

“…The sensitivity and specificity of this SNP threshold for defining linkage varies according to the point during the pandemic at which it is being applied, both in terms of time since the start of the pandemic (greater overall viral diversity afforded by later time points in the pandemic), and the current rate of transmission (locally reduced diversity during exponential periods of spread, such as was observed with the emergence of the alpha variant in the winter of 2020). Improvements in sensitivity and specificity to detect transmission might also be gained from considering patterns of intra-host variation [35,36].…”

Ethical review of COVID-19 vaccination requirements for transplant center staff and patients

“… 14 , 15 , 16 For COVID‐19, there have been confirmed nosocomial outbreaks beginning with asymptomatic healthcare workers or amplified by transmission chains involving healthcare workers resulting in patient illness and death. 17 , 18 Transplant patients are particularly vulnerable, even if they are themselves vaccinated. 19 , 20 , 21 , 22 , 23 Infections among transplant candidates may lead to waitlist inactivation, missed transplant opportunities, or death; infections among transplant recipients may lead to death or graft loss.…”