Remdesivir and GS-441524 Retain Antiviral Activity against Delta, Omicron, and Other Emergent SARS-CoV-2 Variants

Article activity feed

1. Version published to 10.1128/aac.00222-22

   Jun 21, 2022
2. 

   ScreenIT

   Feb 14, 2022

   SciScore for 10.1101/2022.02.09.479840: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The blocking buffer was then aspirated and 50 μL of a 1:4000 dilution of rabbit anti-SARS-CoV-2 nucleocapsid (N) antibody (MA536086, Invitrogen) in blocking buffer was added and incubated for 2 h at 37°C.	anti-SARS-CoV-2 nucleocapsid (N suggested: None MA536086 suggested: (Thermo Fisher Scientific Cat# MA5-36086, RRID:AB_2866697)
   Experimental Models: Cell Lines
   Sentences	Resources
   A549-ACE2 cells that stably express human angiotensin-converting enzyme 2 (hACE2) were established and provided …

   SciScore for 10.1101/2022.02.09.479840: (What is this?)

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

   Table 1: Rigor

   Ethics	not detected.
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The blocking buffer was then aspirated and 50 μL of a 1:4000 dilution of rabbit anti-SARS-CoV-2 nucleocapsid (N) antibody (MA536086, Invitrogen) in blocking buffer was added and incubated for 2 h at 37°C.	anti-SARS-CoV-2 nucleocapsid (N suggested: None MA536086 suggested: (Thermo Fisher Scientific Cat# MA5-36086, RRID:AB_2866697)
   Experimental Models: Cell Lines
   Sentences	Resources
   A549-ACE2 cells that stably express human angiotensin-converting enzyme 2 (hACE2) were established and provided by the University of Texas Medical Branch (46).	A549-ACE2 suggested: None
   All viruses were propagated 1-2 times in Vero-TMPRSS2 cells as follows.	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
   Nucleoprotein ELISA: 3×104 A549-ACE2-TMPRSS2 cells in 100 μL DMEM (supplemented with 10% FBS and 1X penicillin/streptomycin) were seeded into each well of a 96-well plate and incubated overnight.	A549-ACE2-TMPRSS2 suggested: None
   Antiviral activity assessment from recombinant luciferase containing viruses: For Nluc readouts, 1.2×104 A549-hACE2 cells per well were suspended in 50 μL infection medium and seeded into a white clear-bottom 96-well plate (Corning) and incubated overnight at 37°C with 5% CO2.	A549-hACE2 suggested: RRID:CVCL_A5KB)
   Recombinant DNA
   Sentences	Resources
   Site-directed mutagenesis and recombinant virus rescue: To produce recombinant SARS-CoV-2 virus, we utilized a SARS-CoV-2 reverse genetics system previously described (24, 49) that was slightly modified by fusing plasmids F1-F3 single plasmid making it a 3-plasmid reverse genetics system producing infectious virus containing either Nano luciferase (Nluc) or the Firefly luciferase (Fluc) transgene.	F1-F3 suggested: RRID:Addgene_87224)
   Desired substitutions in nsp12 of the SARS-CoV-2 genome were added to the nsp12 containing F4 plasmid using the Quick-Change PCR protocol using Platinum SuperFI II PCR master-mix (ThermoFisher Scientific cat. No. 12361010) following manufacturer’s protocols.	F4 suggested: None
   Software and Algorithms
   Sentences	Resources
   EC50 values were determined using GraphPad Prism 8.1.2 using non-linear regression curve fits.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)

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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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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 10.1101/2022.02.09.479840 on bioRxiv

   Feb 10, 2022