Emergence of N antigen SARS-CoV-2 genetic variants escaping detection of antigenic tests

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1. 

   ScreenIT

   Mar 28, 2021

   SciScore for 10.1101/2021.03.25.21253802: (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.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Typically, 100 µl of not inactivated swab medium were inoculated in monolayers of Vero cells (ATCC CCL-81) with Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 2% (v/v) of fetal bovine serum (FBS) (Gibco) and 1% (v/v) of penicillin/streptomycin (Gibco) and incubated at 37°C with 5% CO2.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   Quality check and mapping of the reads: Raw sequences were filtered for …

   SciScore for 10.1101/2021.03.25.21253802: (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.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Typically, 100 µl of not inactivated swab medium were inoculated in monolayers of Vero cells (ATCC CCL-81) with Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 2% (v/v) of fetal bovine serum (FBS) (Gibco) and 1% (v/v) of penicillin/streptomycin (Gibco) and incubated at 37°C with 5% CO2.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   Quality check and mapping of the reads: Raw sequences were filtered for length and quality with Trimmomatic v0.40 12 according to the following parameters: ILLUMINACLIP:TruSeq3-PE-2:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20 MINLEN:90.	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   High quality reads were aligned on the SARS-CoV-2 reference genome (genbank ACC: NC_045512) with BWA-MEM v0.7.17 13.	BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   Duplicated reads were then removed with Picard tool v2.25.0 (http://broadinstitute.github.io/picard/).	Picard suggested: (Picard, RRID:SCR_006525)
   Consensus sequence were generated using a combination of SAMtools v1.11 14 and VarScan v2.4.1 15 variant caller.	SAMtools suggested: (SAMTOOLS, RRID:SCR_002105) VarScan suggested: (VARSCAN, RRID:SCR_006849)

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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:

   Unfortunately, the nature of the B cell epitope recognized by the antibody utilised in the Abbott test is not known but apparently other SARS-CoV-2 antigen tests, COVID-19 Ag Respi-Strip and LumiraDX SARS-CoV-2, seem to suffer of the same limitation as supernatant of cultured cells infected with virus isolates D1_7_B.1.1.119, D1_8_B.1.177.7, D2_1_B.1.160, and D2_3_B.1.177.4 carrying respectively mutations R209I, P365S, M234I-A376T, and D348Y failed to generate a positive signal thus suggesting that these assays use antibodies with similar specificities. The fact that some virus variants are “undetectable” irrespectively of the Ct value combined with a lower sensitivity of antigen tests may have accounted for the partial and disappointing results obtained when antigen tests were utilised in large population screens. It should also be considered that the massive use of antigen tests could exert a positive selection for undetectable virus variants and thereby causing their relative increase in frequency over time. Our results would support this notion: The DNCOV+/ANCOV- A376T-M241I virus variant accounted for 42% of all mutation found in the N-antigen B cell epitope 337-422. Analysis of virus sequences isolated from January 2020 to December 2020 indicated that in Veneto the A376T-M241I variant progressively increased in frequency from the beginning of October 2020 to 20% by the end of December 2020 while in Europe and the rest of Italy, after a small peak in October 2020, it fol...

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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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   Read the original source
2. 

   Version published to 10.1101/2021.03.25.21253802 on medRxiv

   Mar 26, 2021