City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants
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SciScore for 10.1101/2022.02.16.22269810: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We then identified Single Nucleotide Polymorphisms (SNPs) and insertions/deletions (Indels) from BAM files using samtools (v1.13, (Danecek et al. 2021)) and VarScan (v2.4.4, P < 0.05, all other settings default, (Koboldt et al. 2012)) on 100,000 sequencing reads with an alignment score > 10. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)VarScansuggested: (VARSCAN, RRID:SCR_006849)1.4.1717 (RStudio Team 2021) and R version 4.1.1 (R Core Team 2021) for all statistical analyses and ggplot2 (Wickham 2016) for visualisations. ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: We …
SciScore for 10.1101/2022.02.16.22269810: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources We then identified Single Nucleotide Polymorphisms (SNPs) and insertions/deletions (Indels) from BAM files using samtools (v1.13, (Danecek et al. 2021)) and VarScan (v2.4.4, P < 0.05, all other settings default, (Koboldt et al. 2012)) on 100,000 sequencing reads with an alignment score > 10. samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)VarScansuggested: (VARSCAN, RRID:SCR_006849)1.4.1717 (RStudio Team 2021) and R version 4.1.1 (R Core Team 2021) for all statistical analyses and ggplot2 (Wickham 2016) for visualisations. ggplot2suggested: (ggplot2, RRID:SCR_014601)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: We detected the following sentences addressing limitations in the study:The software developers have acknowledged this limitation, and the design of primers to create appropriate co-occurrence amplicons for relevant sequencing schemes is suggested as a workaround (Jahn et al. 2021). It is important to note that even in cases where co-occurrence analysis is applicable, our fine-scale local data highlighted that wastewater monitoring sometimes detects new variants earlier than clinical testing, but not always. The reasons for this are yet unclear. It is likely that the inherent variability of wastewater detections, due to variations in viral shedding rates and dilution from rainfall, etc (Polo et al. 2020)), and the increasing stochasticity of clinical detection with decreasing population size play a role. Certainly the relationships between population size, wastewater flow variation and SARS-CoV-2 variant detection warrant further investigation. This mixed pattern of wastewater Alpha detections preceding confirmed clinical cases in some parts of Liverpool, yet vice versa in others, highlights the complementarity of the approaches. Wastewater monitoring has the notable advantages of being more cost-effective per unit of population and is less biased by testing frequencies in different communities (Polo et al. 2020), while sequencing of clinical samples provides greater specificity and the opportunity for contact tracing. Indeed, our finding that Alpha was detected in wastewater in North Liverpool much earlier than clinical cases had indicated, corr...
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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