@article{bb96cc9396234df396011552f1b1fae9,
title = "State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness",
abstract = "Background: COVID-19 has affected many healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods: Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings: Between March-October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here, requested for hospital investigations. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of patients that generated numerous secondary infections. Key limitations at the HCF level were identified. Interpretation: Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics. Funding: The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.",
keywords = "Covid-19, Genomic epidemiology, Healthcare workers, Pandemic preparedness",
author = "Watt, {Anne E.} and Sherry, {Norelle L.} and Patiyan Andersson and Lane, {Courtney R.} and Sandra Johnson and Mathilda Wilmot and Kristy Horan and Michelle Sait and Ballard, {Susan A.} and Christina Crachi and Beck, {Dianne J.} and Caroline Marshall and Kainer, {Marion A.} and Rhonda Stuart and Christian McGrath and Kwong, {Jason C.} and Pauline Bass and Kelley, {Peter G.} and Amy Crowe and Stephen Guy and Nenad Macesic and Karen Smith and Williamson, {Deborah A.} and Torsten Seemann and Howden, {Benjamin P.}",
note = "Funding Information: The Microbiological Diagnostic Unit Public Health Laboratory receives funding from the State Government of Victoria. This work was funded by the National Health & Medical Research Council (NHMRC) through the Medical Research Future Fund (MRFF) – Coronavirus Research Response: 2020 Tracking COVID-19 in Australia using Genomics Grant Opportunity (MRF9200006). NLS was supported by an Australian Government Research Training Program (RPT) scholarship (GNT1093468). BPH was supported by an NHMRC Investigator Grant (GNT1196103). Funders had no role in study design, data collection, data analysis, interpretation or writing of the report. Funding Information: We gratefully acknowledge the large number of staff at Victorian healthcare facilities and diagnostic laboratories who collected data and undertook diagnostic testing for COVID-19 in Victoria. We would particularly like to acknowledge the considerable efforts of infection prevention and control staff at affected facilities. We would especially acknowledge the contribution of Terri Butcher and Adrian Tramontana (Western Health), Andrew Stewardson, Allen Cheng, Amanda Dennison, Anton Peleg, and Denis Spelman (Alfred Health), Claire Gordon (Austin Health), Kylie Hall and Alexandra Bonello (Eastern Health), Bradley Gardiner and Suman Majumdar (Epworth), Tony Korman (Monash Health), Victoria Madigan, Barbara Brozic and Madelaine Flynn (Northern Hospital), Susan Gonelli (Peninsula Health), Katherine Bond, Vivian Leung, Chris Bailie, Laura Piu, and Kirsty Buising (Royal Melbourne Hospital), Leilani Knapp, Mary-Jo Waters, Yves Lorenzo and Samantha Palmby (St Vincent's Hospital). Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = aug,
doi = "10.1016/j.lanwpc.2022.100487",
language = "English",
volume = "25",
journal = "The Lancet Regional Health - Western Pacific",
issn = "2666-6065",
publisher = "Elsevier",
}
