Resistance Mutations in SARS-CoV-2 Delta Variant after Sotrovimab Use
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SciScore for 10.1101/2021.12.18.21267628: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical and governance approval for the study was granted by the Western Sydney Local Health District Human Research Ethics Committee (2020/ETH02426) and (2020/ETH00786) SARS-CoV-2 culture: Respiratory tract specimens that had detectable SARS-CoV-2 RNA by RT-PCR were cultured in vero E6 cells expressing transmembrane serine protease 2 (VeroE6/TMPRSS2; JCRB1819) as previously outlined (Supplementary Figure S2).15 Briefly, cell cultures were seeded at 1-3×104 cells/cm2 in Dulbecco’s minimal essential medium (DMEM, Lonza, Basel, Switzerland) supplemented with 9% foetal bovine serum (FBS, HyClone). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power… SciScore for 10.1101/2021.12.18.21267628: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical and governance approval for the study was granted by the Western Sydney Local Health District Human Research Ethics Committee (2020/ETH02426) and (2020/ETH00786) SARS-CoV-2 culture: Respiratory tract specimens that had detectable SARS-CoV-2 RNA by RT-PCR were cultured in vero E6 cells expressing transmembrane serine protease 2 (VeroE6/TMPRSS2; JCRB1819) as previously outlined (Supplementary Figure S2).15 Briefly, cell cultures were seeded at 1-3×104 cells/cm2 in Dulbecco’s minimal essential medium (DMEM, Lonza, Basel, Switzerland) supplemented with 9% foetal bovine serum (FBS, HyClone). Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication Contamination: Routine mycoplasma testing using RT-PCR was performed to exclude cell line mycoplasma contamination and culture work was undertaken under physical containment laboratory level 3 (PC3) biosafety conditions. Table 2: Resources
Software and Algorithms Sentences Resources Sequencing libraries were then sequenced with paired end 76 bp chemistry on the iSeq or MiniSeq (Illumina) platforms. MiniSeqsuggested: NoneBioinformatic analysis: Raw sequence data were processed using an in-house quality control procedure prior to further analysis as described previously.17,18 De-multiplexed reads were quality trimmed using Trimmomatic v0.36 (sliding window of 4, minimum read quality score of 20, leading/trailing quality of 5 and minimum length of 36 after trimming).19 Briefly, reads were mapped to the reference SARS-CoV-2 genome (NCBI GenBank accession MN908947.3) using Burrows-Wheeler Aligner (BWA)-mem version 0.7.1720, with unmapped reads discarded. Trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)BWA)-memsuggested: NoneThe GISAID and New South Wales (NSW) genomes were aligned with MAFFT v7.402 (FFT-NS-2, progressive method). MAFFTsuggested: (MAFFT, RRID:SCR_011811)28 Graphs were generated using RStudio (version 3.6.1) and phylogenetic trees were constructed using the R package ggtree. RStudiosuggested: (RStudio, RRID:SCR_000432)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.
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