학술논문
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
Document Type
article
Author
Anne E. Watt; Norelle L. Sherry; Patiyan Andersson; Courtney R. Lane; Sandra Johnson; Mathilda Wilmot; Kristy Horan; Michelle Sait; Susan A. Ballard; Christina Crachi; Dianne J. Beck; Caroline Marshall; Marion A. Kainer; Rhonda Stuart; Christian McGrath; Jason C. Kwong; Pauline Bass; Peter G. Kelley; Amy Crowe; Stephen Guy; Nenad Macesic; Karen Smith; Deborah A. Williamson; Torsten Seemann; Benjamin P. Howden
Source
The Lancet Regional Health. Western Pacific, Vol 25, Iss , Pp 100487- (2022)
Subject
Language
English
ISSN
2666-6065
Abstract
Summary: 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.