Transmission of SARS-CoV-2 among healthcare workers and patients in a teaching hospital in the Netherlands confirmed by whole-genome sequencing

Abstract

We investigated the sources of infection among healthcare workers (HCWs) and patients in a teaching hospital during the early stages of the COVID-19 pandemic with epidemiological and whole genome sequencing data. This retrospective study is performed in a Dutch teaching hospital with nursing facilities located in Rotterdam and Schiedam with around 45,000 admissions per year. From 3 rd April to 11 th May 2020 88 HCWs and 215 patients were diagnosed with SARS-CoV-2 infection. Whole genome sequences were obtained for 30 HCWs and 20 patients. We found 7 sequence types in HCW and 11 in patients. Sequence Cluster A was the most predominant sequence type detected in 23 (77%) HCW, of whom 14 (74%) had direct patient contact and 9 (90%) with indirect patient contact. In addition, seven patients outside of the COVID-19 cohort isolation ward who became positive during their admission were infected with SARS-CoV-2 cluster A. Following universal masking of all HCWs and emphasis on physical distancing during meals and breaks, no further evidence was found for patient to HCW or HCW-to-HCW transmission or vice versa. The identification of genomic cluster A in patients and HCWs infected with SARS-CoV-2 by whole genome sequencing suggests transmission between HCWs, but also from HCWs to patients.

Use of whole-genome sequencing to investigate a cluster of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in emergency department personnel

“…[3][4][5] However, in the setting of widespread community transmission, sequencing of SARS-CoV-2 is essential as an adjunct to contact tracing to confirm transmission among personnel. 6,9 In the current investigation, sequencing confirmed transmission of SARS-CoV-2 among emergency department personnel but demonstrated that the suspected 6-person outbreak included 2 distinct transmission clusters and 1 unrelated infection. Our results suggest that SARS-CoV-2 variants initially acquired in the community were subsequently spread among hospital personnel.…”

Investigation of intra-hospital SARS-CoV-2 transmission using nanopore whole-genome sequencing

“…Through the employment portable sequencing instruments and rigging an online integrative analysis platform, the protocols, primers and bioinformatics tools devised by the ARTIC network allow for realtime epidemiology of the SARS-CoV-2 outbreak. Yet, only a few studies have been published in which whole genome sequencing (WGS) has been combined with epidemiological data to trace possible transmission chains in health care settings [10][11][12][13][14][15].…”

The Backward Art of Slowing the Spread? Congregation Efficiencies during COVID-19

“…The study authors also emphasized the role of prevention efforts in shaping these outcomes. (Seidelman, et al 2020, Paltansing, et al 2021. Yale University's Emergency Department described "structure[ing] into distinct pods...staggering breaks or using portable computers…taping off or removing chairs" and "individually packaged meals" (Sangal, et al 2020 Although households likely did not implement many of the prevention protocols cited in Table 2, they did reduce their geographic mobility (Chetty, et al 2020).…”

“…If this unknown category were allocated proportionally between community-and work-acquired, the ratios shown in my Figure 3 would not change. 18 Another study of a hospital in the Netherlands (Paltansing, et al 2021) measured in-hospital transmission using whole-genome sequencing. It found only one in-hospital transmission after April 30, 2020, which was the seventh day after implementing universal masking of healthcare workers.…”