Nucleocapsid Antigenemia Is a Marker of Acute SARS-CoV-2 Infection

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1. Version published to 10.1093/infdis/jiac225

   Jul 25, 2022
2. 

   ScreenIT

   Jan 31, 2022

   SciScore for 10.1101/2022.01.23.22269354: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: This study was approved and granted complete HIPAA and consent waiver by the Emory University Institutional Review Board (STUDY00000510).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	The entire medical record was available during this stage, but the reviewer was blinded to antigenemia status which was not considered in labeling of COVID-19 status or category assignment.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Serological Testing: In-house developed single-dilution serological screening assays for SARS-CoV-2 receptor binding domain (RBD) and nucleocapsid antibodies were used to establish serological status at the time of …

   SciScore for 10.1101/2022.01.23.22269354: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	IRB: This study was approved and granted complete HIPAA and consent waiver by the Emory University Institutional Review Board (STUDY00000510).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	The entire medical record was available during this stage, but the reviewer was blinded to antigenemia status which was not considered in labeling of COVID-19 status or category assignment.
   Power Analysis	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Serological Testing: In-house developed single-dilution serological screening assays for SARS-CoV-2 receptor binding domain (RBD) and nucleocapsid antibodies were used to establish serological status at the time of antigenemia testing.	SARS-CoV-2 receptor binding domain (RBD) suggested: None antigenemia testing. suggested: None
   Software and Algorithms
   Sentences	Resources
   The Emory Healthcare Clinical Data Warehouse (CDW) was queried for SARS-CoV-2 nucleic acid amplification tests (NAAT), clinical notes, ICD-10 codes, laboratory values, mechanical ventilation, and date of death.	Emory Healthcare suggested: (One Mind Biospecimen Bank Listing, RRID:SCR_004193)
   Data analysis: Data obtained during specimen collection were stored in Microsoft Excel.	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137)
   All data were then imported into MATLAB (The MathWorks, Inc.) for analysis.	MATLAB suggested: (MATLAB, RRID:SCR_001622)

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   Results from OddPub: Thank you for sharing your data.

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Recognizing these limitations, we performed a post-hoc investigation of outlier cases, which facilitated hypothesis generation regarding reasons for prolonged antigenemia such as reduced renal function, prolonged critical illness, and immune compromise (Supplementary Tables 1-5 & 7). Several studies have demonstrated high specificity of antigenemia by evaluation of pre-pandemic samples [15, 17, 20], suggesting many false positives in our study are likely to have active infection beyond the parameters for acute infection defined in our reference standard schema. This will be further clarified as more robust comparisons to viral culture, sgRNA, RT-PCR Ct value, and respiratory antigen testing can be achieved. Together our data demonstrate that nucleocapsid antigenemia is a sensitive and specific biomarker of acute COVID-19 wherein COVID-19 status is defined by time since earliest positive testing and symptom onset. We conclude that nucleocapsid antigenemia is a promising candidate biomarker for active viral replication – the definition of which is the presence of replication-competent virus in a host – recognizing that the available evidence points to this being an individualized process that cannot be broadly defined based on a timeline. Further prospective studies with rigorous documentation of clinical course and correlation with viral culture and other potential biomarkers of viral replication are needed.

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2022.01.23.22269354v1 on medRxiv

   Jan 27, 2022