Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
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Abstract
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.
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SciScore for 10.1101/2021.08.31.21262938: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Wastewater collection and sequencing from New Haven, CT: Primary sewage sludge samples were collected from the New Haven, CT, USA Wastewater Treatment Plant.
IRB: Clinical sequencing and data processing from New Haven, CT: Ethics statement: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).Sex as a biological variable not detected. Randomization After removing low-quality sequences (defined as having less … SciScore for 10.1101/2021.08.31.21262938: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Field Sample Permit: Wastewater collection and sequencing from New Haven, CT: Primary sewage sludge samples were collected from the New Haven, CT, USA Wastewater Treatment Plant.
IRB: Clinical sequencing and data processing from New Haven, CT: Ethics statement: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599).Sex as a biological variable not detected. Randomization After removing low-quality sequences (defined as having less than 29,500 non-ambiguous nucleotides) we randomly selected 1000 sequences per lineage for further analysis. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources We then used VCFtools to compute allele frequencies within each lineage. VCFtoolssuggested: (VCFtools, RRID:SCR_001235)Clinical sequencing and data processing from New Haven, CT: Ethics statement: The Institutional Review Board from the Yale University Human Research Protection Program determined that the RT-qPCR testing and sequencing of de-identified remnant COVID-19 clinical samples obtained from clinical partners conducted in this study is not research involving human subjects (IRB Protocol ID: 2000028599). Human Research Protection Programsuggested: NoneReads were aligned to a reference genome (GenBank MN908937.3) using BWA-MEM v. BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)Results from OddPub: Thank you for sharing your code and 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.
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