State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers – Insights for Future Pandemic Preparedness
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Abstract
Background
COVID-19 has resulted in many infections in 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 Victorian dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links.
Findings
Between March and October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here. 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 individual patients including super-spreading events. 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.
Article activity feed
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SciScore for 10.1101/2021.09.08.21263057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics: Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.4). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations of the study include the highly clonal nature of cases in Victoria at this time, with >95% of cases from the second wave being seeded for a single tm event. This limited the ability to resolve some transmission networks, particularly …
SciScore for 10.1101/2021.09.08.21263057: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethics: Ethical approval was received from the University of Melbourne Human Research Ethics Committee (study number 1954615.4). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
No key resources detected.
Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Limitations of the study include the highly clonal nature of cases in Victoria at this time, with >95% of cases from the second wave being seeded for a single tm event. This limited the ability to resolve some transmission networks, particularly early in the outbreak, and may erroneously suggest single introductions of a cluster when there may have been multiple introductions from a genomic cluster from the community. This increases the importance of quality epidemiologic data to assist with interpretation of genomic data when performing these analyses. Our investigations were also limited by HCW and patient cases that were not able to be sequenced although numbers were relatively small, and the proportion of cases successfully sequenced was greater than most other jurisdictions. Similar processes could easily be applied to other healthcare systems where genomics is less commonly available; in particular, focussed sequencing of hospitalised cases and HCWs could achieve very similar results, albeit with a small chance of false-positive genomic links due to multiple introductions of the same genomic cluster from the community. The results from each facility have shown that there were multiple contributors to COVID-19 infections in HCWs in Victoria in 2020, and that while there were common factors contributing to transmission across different facilities, each outbreak was in fact a unique combination of contributors and had to be assessed individually. Through our experience wor...
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