Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes
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SciScore for 10.1101/2021.10.22.21265255: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Clinical specimens: Use of deidentified remnant clinical specimens from University of Washington Virology Laboratory (UWVL) for SARS-CoV-2 testing was approved by the University of Washington Institutional Review Board.
Field Sample Permit: Laboratory-confirmed specimens used in this study came from nasal or nasopharyngeal swabs collected in either PBS or viral transport media that had >500 μL volume remaining.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero E6-TMPRSS2 cells (obtained from the JCRB Cell Bank, JCRB … SciScore for 10.1101/2021.10.22.21265255: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Clinical specimens: Use of deidentified remnant clinical specimens from University of Washington Virology Laboratory (UWVL) for SARS-CoV-2 testing was approved by the University of Washington Institutional Review Board.
Field Sample Permit: Laboratory-confirmed specimens used in this study came from nasal or nasopharyngeal swabs collected in either PBS or viral transport media that had >500 μL volume remaining.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Vero E6-TMPRSS2 cells (obtained from the JCRB Cell Bank, JCRB No. JCRB1819) were inoculated with 100 μL of clinical sample, inoculated for 1 hour at 37ºC with rocking, washed with PBS, and overlaid with 1 ml standard Vero media containing 2% FBS. Vero E6-TMPRSS2suggested: NoneSoftware and Algorithms Sentences Resources LDA), Abbott m2000 (Abbott Laboratories, Chicago, IL, USA) Abbott Laboratoriessuggested: NoneSwift SNAP library preparation and quality control: Using SuperScript™ IV First-Strand Synthesis System (ThermoFisher, Waltham, MA, USA), 11 μL of extracted RNA was subjected to single-strand complementary DNA (sscDNA) synthesis, and 10 μL of the resulting sscDNA was used for library preparation using the Swift SARS-CoV-2 SNAP Version 2.0 kit (Swift Biosciences™, Ann Arbor, MI, USA). SNAPsuggested: (SNAP, RRID:SCR_007936)Positive and negative controls were included on each run, and only sequencing runs with > 50% reads passing filter (PF) and > 60% of bases exceeding Phred quality scores of 30 (Q30) were accepted. Phredsuggested: (Phred, RRID:SCR_001017)For Sanger sequencing, reads were imported into Geneious (v9.1.8, Biomatters, Auckland, New Zealand), trimmed with an error probability limit of 0.005, mapped to the reference Spike sequence (NC_045512.2: 21563-25384), and manually trimmed to the start and stop codons for Spike. Geneioussuggested: (Geneious, RRID:SCR_010519)Probit analysis to determine limit of detection calculations was performed in SPSS (v26, IBM, Armonk, NY). SPSSsuggested: (SPSS, RRID:SCR_002865)For SAREPI orders (requested for outbreak/cluster investigations), consensus sequences passing QC criteria are aligned using MAFFT v7.45 and the total number of pairwise nucleotide differences between sequences is reported as a table along with SARSEQ results. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Bioinformatic pipeline validation: To assess the performance of our bioinformatic pipeline and data processing steps, we used a set of benchmark datasets from the CDC (https://github.com/CDCgov/datasets-sars-cov-2). Bioinformaticsuggested: (QFAB Bioinformatics, RRID:SCR_012513)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:One of the limitations of short-read sequencing using reference-based approaches is the reduced ability to identify large structural variants, long indels, and tandem duplicates. Long deletions often manifest as low coverage regions masked with ambiguous bases (Ns) and require manual review to confirm that they are deletions vs. amplicon dropouts. In the current study, we saw one example of this, and we have previously identified similar deletions in ORFs 7a, 7b, and 8 using Swift55. Taken together, our results demonstrate the high sensitivity, specificity, and reproducibility of the Swift SNAP amplicon panel for SARS-CoV-2, which make it ideal for clinical applications. Our protocol is available at https://www.protocols.io/view/uw-virology-swift-snapv2-protocol-byw4pxgw with options for automation via robotic liquid handling systems. In addition, our study provides a framework for validating amplicon sequencing methods which have proved to be an important tool in our fight against COVID-19 and will be for other emerging pathogens.
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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