The Rapid Assessment of Aggregated Wastewater Samples for Genomic Surveillance of SARS-CoV-2 on a City-Wide Scale
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Throughout the course of the ongoing SARS-CoV-2 pandemic there has been a need for approaches that enable rapid monitoring of public health using an unbiased and minimally invasive means. A major way this has been accomplished is through the regular assessment of wastewater samples by qRT-PCR to detect the prevalence of viral nucleic acid with respect to time and location. Further expansion of SARS-CoV-2 wastewater monitoring efforts to include the detection of variants of interest/concern through next-generation sequencing has enhanced the understanding of the SARS-CoV-2 outbreak. In this report, we detail the results of a collaborative effort between public health and metropolitan wastewater management authorities and the University of Louisville to monitor the SARS-CoV-2 pandemic through the monitoring of aggregate wastewater samples over a period of 28 weeks. Through the use of next-generation sequencing approaches the polymorphism signatures of Variants of Concern/Interest were evaluated to determine the likelihood of their prevalence within the community on the basis of their relative dominance within sequence datasets. Our data indicate that wastewater monitoring of water quality treatment centers and smaller neighborhood-scale catchment areas is a viable means by which the prevalence and genetic variation of SARS-CoV-2 within a metropolitan community of approximately one million individuals may be monitored, as our efforts detected the introduction and emergence of variants of concern in the city of Louisville. Importantly, these efforts confirm that regional emergence and spread of variants of interest/concern may be detected as readily in aggregate wastewater samples as compared to the individual wastewater sheds. Furthermore, the information gained from these efforts enabled targeted public health efforts including increased outreach to at-risk communities and the deployment of mobile or community-focused vaccination campaigns.
Article activity feed
-
-
SciScore for 10.1101/2021.08.17.21262170: (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
Software and Algorithms Sentences Resources The reverse transcriptase incubation step was performed with sequential incubation at 23°C for 10 min, 50°C for 30 min, and 80°C for 10 min, according to the manufacturer’s protocol with adjustment of the incubation times recommended by Swift Biosciences SNAP low input protocol. 5.3. Library Preparation: Libraries were prepared using the Swift Biosciences SNAP low input protocol for SARS-CoV-2 (Swift Bioscience, Ann Arbor, MI, Cat # COSG1V2-96, SN-5X296). Swift Biosciencessuggested: NoneLow quality bases … SciScore for 10.1101/2021.08.17.21262170: (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
Software and Algorithms Sentences Resources The reverse transcriptase incubation step was performed with sequential incubation at 23°C for 10 min, 50°C for 30 min, and 80°C for 10 min, according to the manufacturer’s protocol with adjustment of the incubation times recommended by Swift Biosciences SNAP low input protocol. 5.3. Library Preparation: Libraries were prepared using the Swift Biosciences SNAP low input protocol for SARS-CoV-2 (Swift Bioscience, Ann Arbor, MI, Cat # COSG1V2-96, SN-5X296). Swift Biosciencessuggested: NoneLow quality bases were trimmed using Trimmomatic v0.38 (1), and were then aligned to the NC_045512.2 reference genome using bwa mem v 0.7.17-r1188 (2). Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)Results from OddPub: Thank you for sharing your data.
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.
-
-
SciScore for 10.1101/2021.03.18.21253604: (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 The reverse transcriptase incubation step was performed with sequential incubation at 23°C for 10 min, 50°C for 30 min, and 80°C for 10 min, according to the manufacturer’s protocol with adjustment of the incubation times recommended by Swift Biosciences SNAP low input protocol. Swift Biosciencessuggested: NoneThe libraries’ size distribution was checked on the Agilent Bioanalyzer using the DNA High Sensitivity Kit (Agilent Technologies, Cat# 5067-4626). Agilent Bioanalyzersugges…SciScore for 10.1101/2021.03.18.21253604: (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 The reverse transcriptase incubation step was performed with sequential incubation at 23°C for 10 min, 50°C for 30 min, and 80°C for 10 min, according to the manufacturer’s protocol with adjustment of the incubation times recommended by Swift Biosciences SNAP low input protocol. Swift Biosciencessuggested: NoneThe libraries’ size distribution was checked on the Agilent Bioanalyzer using the DNA High Sensitivity Kit (Agilent Technologies, Cat# 5067-4626). Agilent Bioanalyzersuggested: NoneLow quality bases were trimmed using Trimmomatic v0.38 (1), and were then aligned to the NC_045512.2 reference genome using bwa mem v 0.7.17-r1188 (2). Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)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.
-