Wastewater surveillance using ddPCR reveals highly accurate tracking of Omicron variant due to altered N1 probe binding efficiency
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Abstract
Wastewater surveillance for SARS-CoV-2 is being used worldwide to understand COVID-19 infection trends in a community. We found the emergence and rapid timeline for dominance of the Omicron variant was accurately reflected in wastewater when measured with droplet digital (dd)PCR. We were able to distinguish Omicron from the circulating Delta variant because Omicron has a mutation in the N1 probe binding region that diminished the fluorescent signal within individual droplets. The ddPCR platform may be advantageous for wastewater surveillance since analysis of the data can segregate fluorescent signals from different individual templates. In contrast, platforms such as qPCR that rely solely on the intensity of fluorescence for quantification would not distinguish a subset of variants with mutations affecting the reaction and could underestimate SARS-CoV-2 concentrations. The proportion of Omicron in wastewater was tightly correlated to clinical cases in five cities and provided a higher resolution timeline of appearance and dominance (>75%) than sequenced clinical samples, which were limited in less populated areas. Taken together, this work demonstrates wastewater is a reliable metric for tracking SARS-CoV-2 at a population level.
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SciScore for 10.1101/2022.02.18.22271188: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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: 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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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:…
SciScore for 10.1101/2022.02.18.22271188: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. 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: 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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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