S-Variant SARS-CoV-2 Lineage B1.1.7 Is Associated With Significantly Higher Viral Load in Samples Tested by TaqPath Polymerase Chain Reaction
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Abstract
A SARS-CoV-2 variant B1.1.7 containing mutation Δ69/70 has spread rapidly in the United Kingdom and shows an identifiable profile in ThermoFisher TaqPath RT-qPCR, S gene target failure (SGTF). We analyzed recent test data for trends and significance. Linked cycle threshold (Ct) values for respiratory samples showed that a low Ct for ORF1ab and N were clearly associated with SGTF. Significantly more SGTF samples had higher inferred viral loads between 1×107 and 1×108. Our conclusion is that patients whose samples exhibit the SGTF profile are more likely to have high viral loads, which may explain higher infectivity and rapidity of spread.
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SciScore for 10.1101/2020.12.24.20248834: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources The laboratory installed at the University of Birmingham - the design and operation of which has been described earlier [1] relies on the Thermofisher TaqPath RT-QPCR test [2]. Thermofisher TaqPathsuggested: NoneFrequency comparisons, Chi-squared, and Mann-Whitney ‘U’ tests for significance of non-Gaussian distributions between S-gene negative and S-gene positive RT-QPCR results were performed using GraphPad Prism version 5.03. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_0…SciScore for 10.1101/2020.12.24.20248834: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources The laboratory installed at the University of Birmingham - the design and operation of which has been described earlier [1] relies on the Thermofisher TaqPath RT-QPCR test [2]. Thermofisher TaqPathsuggested: NoneFrequency comparisons, Chi-squared, and Mann-Whitney ‘U’ tests for significance of non-Gaussian distributions between S-gene negative and S-gene positive RT-QPCR results were performed using GraphPad Prism version 5.03. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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:Limitations of this data are: At the time of writing, temporal or geographic data is not available for individual samples included in this analysis. Clearly, other Lighthouse centres, NHS or private sector laboratories using the TaqPath test, or indeed other RT-qPCR involving S-gene detection, should add data to this finding to confirm or refute the analysis performed here.
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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SciScore for 10.1101/2020.12.24.20248834: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Frequency comparisons, Chi-squared, and Mann-Whitney ‘U’ tests for significance of non-Gaussian distributions between S-gene negative and S-gene positive RT-QPCR results were performed using GraphPad Prism version 5.03. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: We did not detect open data. We also did not detect open …
SciScore for 10.1101/2020.12.24.20248834: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Frequency comparisons, Chi-squared, and Mann-Whitney ‘U’ tests for significance of non-Gaussian distributions between S-gene negative and S-gene positive RT-QPCR results were performed using GraphPad Prism version 5.03. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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:
Limitations of this data are: (a) Our analysis provides supporting evidence to explain why the S-VoC may be transmitting more rapidly amongst populations, but it does not provide an explanation of how an increased viral load could occur. The biological plausibility of higher infectivity, whether through evolutionary viral replication advantages or evasion of the host immune system, will become apparent through infectivity studies of currently being performed. (b) Although we have made broad inferences in relative viral load in the samples, the TaqPath is not a quantitative assay for SARS-CoV-2 and our observations should be repeated by a dilution series or a validated quantitative method. (c) Our investigation does not directly link the RT-QPCR S-dropout phenomenon to specific viral mutations known to interfere with RT-QPCR detection, and whole genome sequencing of individual samples will prove valuable in strengthening the association with changes in the viral genome. At the time of writing, temporal or geographic data is not available for individual samples included in this analysis. Clearly, other Lighthouse centres, NHS or private sector laboratories using the TaqPath test, or indeed other RT-qPCR involving S-gene detection, should add data to this finding to confirm or refute the analysis performed here.
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.
About SciScore
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