Detection of SARS-CoV-2 Variants Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in Wastewater Settled Solids Using Mutation-Specific Assays Is Associated with Regional Detection of Variants in Clinical Samples
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Wastewater represents a pooled biological sample of the contributing community and thus a resource for assessing community health. Here, we show that emergence, spread, and disappearance of SARS-CoV-2 infections caused by variants of concern are reflected in the presence of variant genomic RNA in wastewater settled solids. This work highlights an important public health use case for wastewater.
Article activity feed
-
-
SciScore for 10.1101/2022.01.17.22269439: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Variants present in regional clinical specimens: The 7-d, centered, rolling average fraction of clinical specimens sequenced from the State of California classified as Alpha, Beta, Gamma, Mu, Lambda, Delta, and Omicron as a function of specimen collection data were acquired through outbreak.info which collates data from GISAID. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Assays were developed in silico using Primer3Plus (https://primer3plus.com/). Primer3Plussuggested: (Primer3Plus, RRID:SCR_003081)Thresholding was carried out using … SciScore for 10.1101/2022.01.17.22269439: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Variants present in regional clinical specimens: The 7-d, centered, rolling average fraction of clinical specimens sequenced from the State of California classified as Alpha, Beta, Gamma, Mu, Lambda, Delta, and Omicron as a function of specimen collection data were acquired through outbreak.info which collates data from GISAID. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Assays were developed in silico using Primer3Plus (https://primer3plus.com/). Primer3Plussuggested: (Primer3Plus, RRID:SCR_003081)Thresholding was carried out using QuantaSoft™ Analysis Pro Software (Bio-Rad, version 1.0.596). QuantaSoft™ Analysis Prosuggested: 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:Despite these limitations, the wastewater variant mutation measurements correlate well with the variant clinical data. SARS-CoV-2 RNA in wastewater is a complex mixture of gRNA of all circulating variants in a given community. SARS-CoV-2 gRNA present in wastewater may be present in an intact or damaged viral capsid with or without an envelope (30), and may have undergone damage or fragmentation (11). In contrast, a clinical specimen contains numerous copies of one SARS-CoV-2 variant, with the gRNA likely intact. Given the complexity of wastewater SARS-CoV-2 gRNA, the presence of a single characteristic mutation in wastewater cannot definitively indicate that a variant is present because a variant is defined by the presence of multiple mutations on a single genome. A single characteristic mutation detected in a wastewater sample could theoretically be from a different variant, known or unknown, containing the same mutation. Even the detection of two mutations characteristic of a specific variant in wastewater does not prove the variant is present, because those two mutations could have originated from different genomes. Moreover, the characteristic mutations used in this study are not present in 100% of the associated variant genomes. Despite these limitations, our results suggest that the concentration of a single mutation characteristic of a variant of concern over the concentration of a conserved SARS-CoV-2 target (the N gene) is associated with the proportion of regional i...
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.
-
