Quantitative SARS-CoV-2 Alpha Variant B.1.1.7 Tracking in Wastewater by Allele-Specific RT-qPCR

Article activity feed

1. Version published to 10.1021/acs.estlett.1c00375

   Jul 18, 2021
2. 

   ScreenIT

   Mar 31, 2021

   SciScore for 10.1101/2021.03.28.21254404: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   All the sequences were aligned to the SARS-CoV-2 reference genome (NC_045512.2) using mafft v7.467 to detect the differences of three target mutations in SARS-CoV-2 spike protein (Katoh & Standley, 2013).	mafft suggested: (MAFFT, RRID:SCR_011811)
   Data analysis: Data was analysed using Microsoft Excel and Graphpad prism.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137) Graphpad suggested: (GraphPad, RRID:SCR_000306)
   Linear regression was performed using Graphpad Prism.	Graph…

   SciScore for 10.1101/2021.03.28.21254404: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   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
   All the sequences were aligned to the SARS-CoV-2 reference genome (NC_045512.2) using mafft v7.467 to detect the differences of three target mutations in SARS-CoV-2 spike protein (Katoh & Standley, 2013).	mafft suggested: (MAFFT, RRID:SCR_011811)
   Data analysis: Data was analysed using Microsoft Excel and Graphpad prism.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137) Graphpad suggested: (GraphPad, RRID:SCR_000306)
   Linear regression was performed using Graphpad Prism.	Graphpad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Results from wastewater samples were analyzed and visualized using Python v3.9.	Python suggested: (IPython, RRID:SCR_001658)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   There are several important challenges and limitations to consider during interpretation of datasets obtained by the AS-qPCR assays we have described here. First, even though this assay has the potential of tracking the spread and presence of B.1.1.7 on the community level, it remains to be determined if these could be extrapolated to incidence of infection with B.1.1.7 and non-B.1.1.7 strains. For example, differences in virus shedding rates between patients carrying B.1.1.7 versus other strains have not yet been robustly determined, though early evidence does suggest that excretion rates may be higher for the VOC (Kissler et al., 2021). Second, the assays presented here allow for the detection of B.1.1.7 by targeting three mutations. While these are currently highly and solely indicative of the B.1.1.7 VOC, there could be the possibility of detecting emerging strains that may possess the same mutations while constituting a VOC of their own. Nonetheless, the proposed AS RT-qPCR assays can be quickly modified and updated to follow the evolution of B.1.1.7 sequences or other VOCs. Finally, the highly specific and targeted nature of this AS RT-qPCR approach does not allow for its usage to discover new variants. However, the presented method allows for a synergy between clinical genomic surveillance and WBE, where new VOCs can be identified locally via clinical surveillance, followed up with rapid development of AS RT-qPCR assays to target VOC-specific mutations, and finally ado...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2021.03.28.21254404 on medRxiv

   Mar 29, 2021