Optimizing SARS-CoV-2 Variant of Concern Screening: Experience from British Columbia, Canada, Early 2021
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Abstract
Comprehensive and timely testing is required for SARS-CoV-2 variant of concern (VoC) screening. Whole genome sequencing (WGS) provides the broadest means to detect circulating VoCs, but requires longer turnaround time than targeted molecular testing by quantitative polymerase chain reaction (qPCR). We demonstrated the feasibility of a combined testing approach for VoC prevalence assessment in British Columbia, and showed high concordance between qPCR testing and WGS. This directly informed wider VoC screening strategy implementation, and public health efforts.
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SciScore for 10.1101/2021.03.23.21253520: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This work was conducted under the public health mandate and institutional review board approval was waived. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources A combined VoC testing strategy based on direct WGS and targeted N501Y mutation qPCR was employed to estimate point prevalence (Appendix Figure 1) based on samples resulted as positive for SARS-CoV-2 from January 30th to February 5th 2021. WGSsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open …
SciScore for 10.1101/2021.03.23.21253520: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This work was conducted under the public health mandate and institutional review board approval was waived. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources A combined VoC testing strategy based on direct WGS and targeted N501Y mutation qPCR was employed to estimate point prevalence (Appendix Figure 1) based on samples resulted as positive for SARS-CoV-2 from January 30th to February 5th 2021. WGSsuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:However, a limitation of this approach is that emergence of variants devoid of N501Y mutation such as the recently-recognized B.1.525, reported here, may be underestimated due to failure of detection by qPCR targets employed, and requires alternative qPCR assays for identification (9, 10). In summary, this study demonstrated the feasibility of a combined targeted and WGS testing strategy for VoC prevalence assessment in one Canadian province, which will be instrumental for continued VoC surveillance, and to inform public health efforts.
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.
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