SARS-CoV-2 evolution during treatment of chronic infection
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SciScore for 10.1101/2020.12.05.20241927: (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
Antibodies Sentences Resources The SARSCOV-2 Spike proteins were visualized by a ChemiDoc® MP imaging system (Biorad) using anti-Spike S2 (Invitrogen) and anti-p24 Gag antibodies. anti-Spike S2suggested: (Imported from the IEDB Cat# S2, RRID:AB_2833224)anti-p24 Gag antibodies.suggested: NoneTesting of convalescent plasma for antibody titres: The Anti-SARS-CoV-2 ELISA (IgG) assay used to test CP for antibody titres was Euroimmun Medizinische Labordiagnostika AG. Anti-SARS-CoV-2 ELISA (IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources This indirect ELISA based assay uses a recombinant structural spike 1 (S1) protein … SciScore for 10.1101/2020.12.05.20241927: (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
Antibodies Sentences Resources The SARSCOV-2 Spike proteins were visualized by a ChemiDoc® MP imaging system (Biorad) using anti-Spike S2 (Invitrogen) and anti-p24 Gag antibodies. anti-Spike S2suggested: (Imported from the IEDB Cat# S2, RRID:AB_2833224)anti-p24 Gag antibodies.suggested: NoneTesting of convalescent plasma for antibody titres: The Anti-SARS-CoV-2 ELISA (IgG) assay used to test CP for antibody titres was Euroimmun Medizinische Labordiagnostika AG. Anti-SARS-CoV-2 ELISA (IgGsuggested: NoneExperimental Models: Cell Lines Sentences Resources This indirect ELISA based assay uses a recombinant structural spike 1 (S1) protein of SARS-CoV-2 expressed in the human cell line HEK 29 for the detection of SARS-CoV2 IgG. HEK 29suggested: NoneVirus neutralisation assays were performed on 293T cell transiently transfected with ACE2 and TMPRSS2 using SARS-CoV-2 Spike pseudotyped virus expressing luciferase48. 293Tsuggested: NonemAb pseudotype neutralisation assay: Virus neutralisation assays were performed on HeLa cells stably expressing ACE2 and using SARS-CoV-2 Spike pseudotyped virus expressing luciferase as previously described49. HeLasuggested: NoneThen, freshly trypsinized HeLa ACE2-expressing cells were added to each well. HeLa ACE2-expressingsuggested: NoneSoftware and Algorithms Sentences Resources For short-read sequencing, FASTQs were downloaded, poor-quality reads were identified and removed, and both Illumina and PHiX adapters were removed using TrimGalore v0.6.6 28. TrimGaloresuggested: NoneBAM files were then sorted and indexed with samtools v1.11 and PCR optical duplicates removed using Picard (http://broadinstitute.github.io/picard). samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Picardsuggested: (Picard, RRID:SCR_006525)All sequences were aligned to the SARS-CoV-2 reference strain MN908947.3, using MAFFT v7.475 with automatic flavour selection34. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Maximum likelihood phylogenetic trees were produced using the above curated dataset using IQ-TREE v2.1.236. IQ-TREEsuggested: (IQ-TREE, RRID:SCR_017254)All trees were visualised with Figtree v. Figtreesuggested: (FigTree, RRID:SCR_008515)In-depth allele frequency variant calling: The SAMFIRE package39 was used to call allele frequency trajectories from BAM file data. SAMFIREsuggested: NoneThe Mathematica software package was to conduct a regression analysis of pairwise sequence distances against time, leading to an estimate of a mean rate of within-host sequence evolution. Mathematicasuggested: (Wolfram Mathematica, RRID:SCR_014448)To corroborate any findings, ClonalFrameML v1.12 42 was also used to infer recombination breakpoints. ClonalFrameMLsuggested: (Clonalframe, RRID:SCR_016060)Structural Viewing: The Pymol Molecular Graphics System v2.4.0 (https://github.com/schrodinger/pymol-open-source/releases) was used to map the location of the four spike mutations of interested onto a SARS-CoV-2 spike structure visualised by Wrobel et al (PDB: 6ZGE)43. Pymolsuggested: (PyMOL, RRID:SCR_000305)IC50 values were calculated in GraphPad Prism. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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.
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