Severe Acute Respiratory Syndrome Coronavirus 2 Total and Subgenomic RNA Viral Load in Hospitalized Patients
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Abstract
Background
Previous studies demonstrated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be detected for weeks after infection. The significance of this finding is unclear and, in most patients, does not represent active infection. Detection of subgenomic RNA has been proposed to represent productive infection and may be a useful marker for monitoring infectivity.
Methods
We used quantitative reverse-transcription polymerase chain reaction (RT-qPCR) to quantify total and subgenomic nucleocapsid (sgN) and envelope (sgE) transcripts in 185 SARS-CoV-2–positive nasopharyngeal swab samples collected on hospital admission and to relate to symptom duration.
Results
We find that all transcripts decline at the same rate; however, sgE becomes undetectable before other transcripts. The median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic compared to total RNA, suggesting that subgenomic transcript copy number is dependent on copy number of total transcripts. The mean difference between total and sgN is 16-fold and the mean difference between total and sgE is 137-fold. This relationship is constant over duration of symptoms, allowing prediction of subgenomic copy number from total copy number.
Conclusions
Subgenomic RNA may be no more useful in determining infectivity than a copy number threshold determined for total RNA.
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SciScore for 10.1101/2021.02.25.21252493: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study protocol was reviewed and approved by the University of Michigan Institutional Review Board (IRB).
Consent: The IRB determined the study to be exempt from requirement for informed consent given retrospective nature of this study and this use of stored biospecimens and deidentified data.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HuH-7 cells were infected with SARS-CoV-2 strain WA-1. HuH-7suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)Software and Algorithms Sentences Res… SciScore for 10.1101/2021.02.25.21252493: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study protocol was reviewed and approved by the University of Michigan Institutional Review Board (IRB).
Consent: The IRB determined the study to be exempt from requirement for informed consent given retrospective nature of this study and this use of stored biospecimens and deidentified data.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources HuH-7 cells were infected with SARS-CoV-2 strain WA-1. HuH-7suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)Software and Algorithms Sentences Resources Simple linear regression and Kaplan-Meier analysis were performed using SPSS software version 27 SPSSsuggested: (SPSS, RRID:SCR_002865)7 (IBM Corporation) and GraphPad (Prism). GraphPadsuggested: (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: 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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