Infectious Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Virus in Symptomatic Coronavirus Disease 2019 (COVID-19) Outpatients: Host, Disease, and Viral Correlates

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1. Version published to 10.1093/cid/ciab968

   Nov 23, 2021
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   Version published to 10.1101/2021.05.28.21258011v2 on medRxiv

   Jun 25, 2021
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   ScreenIT

   Jun 4, 2021

   SciScore for 10.1101/2021.05.28.21258011: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All study participants provided written informed consent.
   Sex as a biological variable	Participants who received a SARS-CoV-2 vaccine, treatment with possible anti-SARS-CoV-2 therapies within 30 days prior to enrollment, and women who were pregnant or breastfeeding were excluded.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Heat inactivated 40x diluted specimen was incubated in the RBD-captured wells, and bound antigen detected using HRP conjugated anti-goat total (IgG, IgM and IgA) or individual antibody isotype on a microplate reader.	anti-goat total (IgG suggested: None
   SARS…

   SciScore for 10.1101/2021.05.28.21258011: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All study participants provided written informed consent.
   Sex as a biological variable	Participants who received a SARS-CoV-2 vaccine, treatment with possible anti-SARS-CoV-2 therapies within 30 days prior to enrollment, and women who were pregnant or breastfeeding were excluded.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Heat inactivated 40x diluted specimen was incubated in the RBD-captured wells, and bound antigen detected using HRP conjugated anti-goat total (IgG, IgM and IgA) or individual antibody isotype on a microplate reader.	anti-goat total (IgG suggested: None
   SARS-CoV-2 antibody positive status was determined by a positive result on at least one of the following: total Ig, IgG, IgM, or IgA.	Ig, IgG suggested: None IgA suggested: None
   A chi-squared test was used to compare inflammatory markers (D-dimer, CRP) by infectious virus status, and by antibody status.	D-dimer, CRP suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   To measure viral RNA, qRT-PCR was performed on NP swabs using CDC primer/probe solution against the N1 region of the nucleocapsid gene (2019-nCoV_N1) at Covance CLS with Promega Maxwell for RNA extraction, manual plate build, and Quantstudio 12kflex for the 96 well qRT-PCR format (lower limit of quantification: 1,018 copies/mL).(17) To measure the presence of infectious virus in each NP swab, samples were cultured in Vero E6 cells similar to prior studies.	Vero E6 suggested: RRID:CVCL_XD71)
   Briefly, VTM samples were thawed, diluted 1:1 in infection medium (MEM, 4% fetal bovine serum, 1X penicillin and streptomycin), and added in duplicate to Vero cell cultures plated 24hr prior.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   (11) On 2 and 5 days post inoculation (dpi), culture positivity was determined by measuring viral RNA in heat inactivated culture medium by qRT-PCR using the Abbott m2000sp/rt quantitative SARS-CoV-2 RNA assay (limit of quantification: 100 copies/mL).	Abbott suggested: (Abbott, RRID:SCR_010477)

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   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).

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

   Importantly, most outpatients with mild-to-moderate symptoms, even those in higher risk groups, have a relatively low probability of developing severe COVID-19 disease.(25–27) While this study describes novel links between virologic and immunologic factors associated with isolation of infectious virus, there are important limitations to consider, including representation. There were a large number of participants who identified as Latinx, yet there was an under-representation of African-Americans and Asian-Americans compared with the US burden of COVID-19.(28) Further, this study enrolled predominantly low risk outpatients with at least one symptom of COVID-19, which limits the study population to outpatients with mild-to-moderate COVID-19. Additional research is needed to understand the factors associated with infectious virus among asymptomatic individuals. While prior studies have demonstrated prolonged virus isolation in hospitalized individuals,(11,23,29) it remains important to identify the factors associated with progression to severe disease and infectious virus shedding in outpatients. Another limitation is that seropositivity is not synonymous with virus neutralization. We observed three antibody positive participants (each had IgM; two had IgG) with positive infectious virus culture, two of whom also had RNA levels above 6.0 log10 but neutralization titers were not available. We also explicitly acknowledge that a negative culture does not exclude the presence of in...

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   Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04405570	Completed	A Safety, Tolerability and Efficacy of Molnupiravir (EIDD-28…

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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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   Read the original source
4. 

   Version published to 10.1101/2021.05.28.21258011v1 on medRxiv

   Jun 1, 2021