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
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Abstract
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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...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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