Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/30313
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.
Austin Authors: Watt, Anne E;Sherry, Norelle L ;Andersson, Patiyan;Lane, Courtney R;Johnson, Sandra;Wilmot, Mathilda;Horan, Kristy;Sait, Michelle;Ballard, Susan A;Crachi, Christina;Beck, Dianne J;Marshall, Caroline;Kainer, Marion A;Stuart, Rhonda;McGrath, Christian;Kwong, Jason C ;Bass, Pauline;Kelley, Peter G;Crowe, Amy;Guy, Stephen;Macesic, Nenad;Smith, Karen;Williamson, Deborah A;Seemann, Torsten;Howden, Benjamin P 
Affiliation: Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia..
Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia..
Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia..
Department of Infectious Diseases, Epworth Hospital, Richmond, Victoria, Australia..
Centre for Research and Evaluation, Ambulance Victoria, Victoria, Australia..
Department of Epidemiology and Preventive Medicine, Monash University, Victoria, Australia..
Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia..
Infectious Diseases
Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia..
Department of Infectious Diseases, Western Health, Footscray, Victoria, Australia..
Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia..
South East Public Health Unit, Monash Health, Clayton, Victoria, Australia..
Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia..
Department of Infectious Diseases, The Northern Hospital, Epping, Victoria, Australia..
Infection Prevention and Healthcare Epidemiology Department, Alfred Health, Prahran, Victoria, Australia..
Department of Infectious Diseases, Peninsula Health, Frankston, Victoria, Australia..
Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia..
Department of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia..
Eastern Health Clinical School, Monash University, Victoria, Australia..
Issue Date: 3-Jun-2022
Date: 2022-08
Publication information: The Lancet regional health. Western Pacific 2022; 25: 100487
Abstract: 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. 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. 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. 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. The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
URI: https://ahro.austin.org.au/austinjspui/handle/1/30313
DOI: 10.1016/j.lanwpc.2022.100487
ORCID: 0000-0002-7789-8360
0000-0002-6298-7942
0000-0003-0237-1473
Journal: The Lancet regional health. Western Pacific
PubMed URL: 35677391
PubMed URL: https://pubmed.ncbi.nlm.nih.gov/35677391/
Type: Journal Article
Subjects: Covid-19
Genomic epidemiology
Healthcare workers
Pandemic preparedness
Appears in Collections:Journal articles

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