SARS-CoV-2 transmission among health care workers, an outbreak investigation using whole-genome sequencing

PLOS ONE RESEARCH ARTICLE SARS-CoV-2 transmission among health care workers, an outbreak investigation using whole-genome sequencing K. S. te Paske ID1☯*, C. van Tienen2‡, D Dunk2,3‡, D. van Pelt4‡, P. W. Smit2,3☯ a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Department of Infectious Disease Control, Municipal Health Service Haaglanden, The Hague, the Netherlands, 2 Department of Medical Microbiology, Maasstad Hospital, Rotterdam, the Netherlands, 3 Molecular Diagnostic Unit, Maasstad Hospital, Rotterdam, the Netherlands, 4 Department of Occupational Health, Maasstad Hospital, Rotterdam, the Netherlands ☯ These authors contributed equally to this work. ‡ These authors also contributed equally to this work * Abstract OPEN ACCESS Citation: te Paske KS, Tienen Cv, Dunk D, Pelt Dv, Smit PW (2023) SARS-CoV-2 transmission among health care workers, an outbreak investigation using whole-genome sequencing. PLoS ONE 18(3): e0283292. https://doi.org/10.1371/journal. pone.0283292 Editor: Kelli L. Barr, University of South Florida, UNITED STATES Received: December 2, 2022 Accepted: February 27, 2023 Background We report an outbreak investigation to map intra-hospital transmission among health care workers (HCW) using epidemiological and whole-genome sequencing data. Methods Fourteen clinical wards (COVID-19 and non-COVID-19) with high infection rates of SARSCoV-2 among HCW were selected and demographical, epidemiological and sequencing data were collected of all HCW testing positive by RT-PCR. Clustered cases were identified based on first disease onsets and differences in single nucleotide polymorphisms (SNP’s) and were analysed for additional characteristics. Published: March 31, 2023 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0283292 Copyright: © 2023 te Paske et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: On https://gisaid.org researchers can download all of the sequencing data that is used in this article. However one has to register (free). Our data is named as follows: Results Data was collected for 123 HCW. Out of 123 HCW, 65 (53%) worked at eight non-COVID19 wards, 56 (46%) at four COVID-19 wards, one (<1%) worked on several wards and for one (<1%) it was unknown. One major cluster (n = 34) and three minor clusters (n = 2,3,4; total n = 9) comprising of 43 HCW (35%) were found after comparing our study population (n = 123) with the circulating regional sequences (n = 819). In clustered cases work was most often the suspected source of infection and continuing work while having symptoms occurred in all clusters, ranging from 1–6 days. Conclusion Our findings strongly indicate transmission of SARS-CoV-2 among HCW. Whole-genome sequencing is useful for identification of clusters and can give direction to targeted infection prevention measures. PLOS ONE | https://doi.org/10.1371/journal.pone.0283292 March 31, 2023 1/6 PLOS ONE "hCoV-19/Netherlands/ZH-MZ-1/2020" up until –> "hCoV-19/Netherlands/ZH-MZ-123/2020". Funding: The author(s) received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. SARS-CoV-2 transmission among health care workers Background Ever since the first reported case of COVID-19 in February 2020, the Netherlands is dealing with SARS-CoV-2 and its consequences. The second wave started in July followed by a steep rise in new daily cases up to 11.000 in December 2020 [1]. National public health measures were repeatedly intensified and the national testing capacity was constrained due to high demands [2]. Large numbers of COVID-19 infections among patients and health care workers (HCW) have posed pressure on all hospitals. Several studies indicate intra-hospital transmission between HCW [3,4]. In response to high infection rates in various clinical wards in one hospital in the Netherlands, we conducted an epidemiological and genomic outbreak investigation of hospital personnel with COVID-19 to gain insight in intra-hospital transmission. Methods Hospital context This study was performed at one hospital in the Netherlands, during 4 September—31 December 2020. At the time, 6468 hospital employees were employed and 3724 RT-PCR tests were performed (personnel only) of which 2324 unique employees (S1 Table). According to hospital policy, all HCW experiencing symptoms consistent with COVID-19 underwent oro-nasopharyngeal swab RT-PCR testing and were instructed to self-isolate. Awaiting test results, HCW were allowed to work with a surgical mask (type 2R) provided that symptoms were mild and their work was considered crucial (irreplaceable, indispensable and working remotely impossible) for continuity of patient care. In case HCW tested positive, they remained on sick leave until seven or fourteen days (depending on severity of clinical course) after disease onset and >24 hours free of symptoms. In case mild symptoms remained present, HCW resumed work after a positive SARS-CoV-2 antibodies test (Wantai, Beijing, China) at day 10. Personal protective equipment supplies and laboratory testing capacity for personnel were sufficient. Study design Fourteen clinical wards (COVID-19 and non-COVID-19) with positive HCW were selected and all HCW working in these wards who tested positive for SARS-CoV-2 were enrolled. Departments with a high likeliness of receiving COVID-19 patients were registered as COVID-19 wards and the remaining departments as non-COVID-19 wards. The molecular diagnostic unit performed RT-PCR testing for SARS-CoV-2 and whole genome sequencing. The occupational health department inventoried demographical and epidemiological data of positive HCW. The Medical Research Ethics Committees United (MEC-U) waived the need for ethical approval as samples were collected for routine diagnostic care. Samples and data were processed anonymously to ensure privacy of our co-workers. Whole genome sequencing and phylogenetic analysis RT-PCR was performed on a fast RT-PCR platform (NeumoDx, Qiagen, Germany). Samples with a cycle threshold below 30 were considered for sequencing. Oxford Nanopore MinION sequencing was performed following ARTICv3 (LoCost) protocol [5], using R9.04.01 flow cells on a MinIon Mk1b or Mk1C device. Basecalling and demultiplexing was performed using Guppy and further analysed using medaka for consensus and variant calling according to the ARTIC pipeline [6]. Phylogenetic analysis and data visualization was done in Pathogen.watch [7]. PLOS ONE | https://doi (...truncated)