Susceptibility of domestic swine to experimental infection with SARS-CoV-2

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1. 

   ScreenIT

   Sep 16, 2020

   SciScore for 10.1101/2020.09.10.288548: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Ethics Statement: Experimental design, including housing conditions, sampling regimen, and humane endpoints, were approved by the Animal Care Committee of the Canadian Science Centre for Human and Animal Health in AUD #C-20-005 and all procedures and housing conditions were in strict accordance with the Canadian Council on Animal Care (CCAC) guidelines.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	Animal numbers were not based on power analysis but on the limitations of the containment animal room size and requirements of CCAC guidelines.
   Sex as a biological variable	Study design: Nineteen domestic, American Yorkshire crossbred pigs (Sus …

   SciScore for 10.1101/2020.09.10.288548: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IACUC: Ethics Statement: Experimental design, including housing conditions, sampling regimen, and humane endpoints, were approved by the Animal Care Committee of the Canadian Science Centre for Human and Animal Health in AUD #C-20-005 and all procedures and housing conditions were in strict accordance with the Canadian Council on Animal Care (CCAC) guidelines.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	Animal numbers were not based on power analysis but on the limitations of the containment animal room size and requirements of CCAC guidelines.
   Sex as a biological variable	Study design: Nineteen domestic, American Yorkshire crossbred pigs (Sus scrufa) (6 castrated males and 13 females, age 8 weeks) were locally sourced in Manitoba, Canada and utilized in this study.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Serum Neutralization Assays: Neutralizing antibody titers in sera were determined via plaque reduction neutralization test against SARS-CoV-2.	SARS-CoV-2 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Each virus-serum mixture was then added to duplicate wells of Vero E6 cells in a 48-well format, incubated for 1 hour at 37°C, and overlaid with 500 μl of 2.0% carboxymethylcellulose in DMEM per well.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Sequences were analysed using an in-house nf-villumina (v2.0.0) Nextflow workflow that performed: read quality filtering with fastp; taxonomic classification with Centrifuge and Kraken2 using a Centrifuge index of NCBI nt downloaded 2020-02-04 and a Kraken2 index of NCBI RefSeq sequences of archaea, bacteria, viral and the human genome GRCh38 downloaded and built on 2019-03-22; removal of non-viral reads (NCBI taxonomic id 10239) using the Kraken2 and Centrifuge taxonomic classification results; de novo assembly by Shovill, Unicycler and Megahit using the taxonomically filtered reads; nucleotide BLAST search of all assembled contigs against NCBI nucleotide downloaded 2020-04-10. nf-villumina	RefSeq suggested: (RefSeq, RRID:SCR_003496) BLAST suggested: (BLASTX, RRID:SCR_001653)

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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:

   • 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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2. 

   Version published to 10.1101/2020.09.10.288548 on bioRxiv

   Sep 10, 2020