A Multitrait Locus Regulates Sarbecovirus Pathogenesis

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1. 

   ScreenIT

   Jun 4, 2022

   SciScore for 10.1101/2022.06.01.494461: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: All virological studies were conducted under BSL3 conditions, and personnel wore appropriate personal protective gear. IACUC: Mouse studies and in vivo infections: Mouse studies were performed at the University of North Carolina (Animal Welfare Assurance #A3410-01) using protocols approved by the UNC Institutional Animal Care and Use Committee (IACUC).
   Sex as a biological variable	First, F1 mice between CC011 and CC074 were generated by cross males and females in both directions, and then the F2 mice were bred in all 4 possible F1 x F1 combinations, to ensure appropriately balanced sex Chromosome and parent-of-origin effects.
   Randomization	F2 mice (226 males, 177 females) …

   SciScore for 10.1101/2022.06.01.494461: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: All virological studies were conducted under BSL3 conditions, and personnel wore appropriate personal protective gear. IACUC: Mouse studies and in vivo infections: Mouse studies were performed at the University of North Carolina (Animal Welfare Assurance #A3410-01) using protocols approved by the UNC Institutional Animal Care and Use Committee (IACUC).
   Sex as a biological variable	First, F1 mice between CC011 and CC074 were generated by cross males and females in both directions, and then the F2 mice were bred in all 4 possible F1 x F1 combinations, to ensure appropriately balanced sex Chromosome and parent-of-origin effects.
   Randomization	F2 mice (226 males, 177 females) were weaned such that littermates were randomized to different experimental cages to reduce litter- or batch-effects on the study, and mice were transferred at 5-6 weeks of age to the laboratory for infection between 9-12 weeks of age.
   Blinding	For Matute-Bello scoring samples were blinded and three random fields of lung tissue were chosen and scored for the following: (A) neutrophils in alveolar space (none = 0, 1–5 cells = 1, > 5 cells = 2), (B) neutrophils in interstitial space (none = 0, 1–5 cells = 1, > 5 cells = 2), (C) hyaline membranes (none = 0, one membrane = 1, > 1 membrane = 2), (D) Proteinaceous debris in air spaces (none = 0, one instance = 1, > 1 instance = 2), (E) alveolar septal thickening (< 2Å∼ mock thickness = 0, 2–4Å∼ mock thickness = 1, > 4Å∼ mock thickness = 2).
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cells were incubated with antibodies against the following markers: efluor506 Viability Dye (Thermo Fisher, 65-0866-14), BUV395 anti-CD45 (Clone 30-F11, BD Biosciences), BV711	anti-CD45 suggested: (BD Biosciences Cat# 740725, RRID:AB_2740403)
   Experimental Models: Cell Lines
   Sentences	Resources
   For virus titration, the caudal lobe of the right lung was homogenized in PBS, resulting homogenate was serial-diluted and inoculated onto confluent monolayers of Vero E6 cells (ATCC CCL-81), followed by agarose overlay.	Vero E6 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   For studies in genetically defined knockout mice, 15-week old CCR9-/- mice (strain 027041), 15-week old CXCR6-/- mice (strain 005693) 15-week old female C57BL/6NJ mice (strain 005304), and 15-week old C57BL/6J (strain 000664) were purchased from Jackson Laboratory, and the genotype of these mutant mice were confirmed via genotyping on the MiniMUGA array (Neogen, Inc.	CCR9-/- suggested: None CXCR6-/- suggested: None C57BL/6NJ suggested: RRID:IMSR_JAX:005304) C57BL/6J suggested: RRID:IMSR_JAX:000664)
   CXCR6-/-, CCR9-/-, and appropriate C57BL/6 control mice were inoculated intranasally with 1×105 PFU of either SARS-CoV MA15, SARS-CoV-2 MA10, or HKU3-SRBD MA in 50 μl of PBS. Body weight, mortality, and pulmonary function by whole body plethysmography (56) were monitored daily as indicated.	C57BL/6 suggested: None
   Software and Algorithms
   Sentences	Resources
   Cells were incubated with antibodies against the following markers: efluor506 Viability Dye (Thermo Fisher, 65-0866-14), BUV395 anti-CD45 (Clone 30-F11, BD Biosciences), BV711	BD Biosciences suggested: (BD Biosciences, RRID:SCR_013311)
   Data were acquired on a flow cytometer (BD-X20; BD Biosciences) and analyzed using FlowJo software (Tree Star) (Figure S5).	FlowJo suggested: (FlowJo, RRID:SCR_008520)

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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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   Read the original source
2. 

   Version 1 published on bioRxiv

   Jun 2, 2022