Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species

  1. Alexandra Schäfer
  2. Lisa E. Gralinski
  3. Sarah R. Leist
  4. Emma S. Winkler
  5. Brea K. Hampton
  6. Michael A. Mooney
  7. Kara L. Jensen
  8. Rachel L. Graham
  9. Sudhakar Agnihothram
  10. Sophia Jeng
  11. Steven Chamberlin
  12. Timothy A. Bell
  13. D. Trevor Scobey
  14. Laura A. VanBlargan
  15. Larissa B. Thackray
  16. Pablo Hock
  17. Darla R. Miller
  18. Ginger D. Shaw
  19. Fernando Pardo Manuel de Villena
  20. Shannon K. McWeeney
  21. Stephanie A. Montgomery
  22. Michael S. Diamond
  23. Mark T. Heise
  24. Vineet D. Menachery
  25. Martin T. Ferris
  26. Ralph S. Baric

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Sarbecovirus (CoV) infections, including Severe Acute Respiratory CoV (SARS-CoV) and SARS-CoV-2, are considerable human threats. Human GWAS studies have recently identified loci associated with variation in SARS-CoV-2 susceptibility. However, genetically tractable models that reproduce human CoV disease outcomes are needed to mechanistically evaluate genetic determinants of CoV susceptibility. We used the Collaborative Cross (CC) and human GWAS datasets to elucidate host susceptibility loci that regulate CoV infections and to identify host quantitative trait loci that modulate severe CoV and pan-CoV disease outcomes including a major disease regulating loci including CCR9. CCR9 ablation resulted in enhanced titer, weight loss, respiratory dysfunction, mortality, and inflammation, providing mechanistic support in mitigating protection from severe SARS-CoV-2 pathogenesis across species. This study represents a comprehensive analysis of susceptibility loci for an entire genus of human pathogens conducted, identifies a large collection of susceptibility loci and candidate genes that regulate multiple aspects type-specific and cross-CoV pathogenesis, and also validates the paradigm of using the CC platform to identify common cross-species susceptibility loci and genes for newly emerging and pre-epidemic viruses.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.05.14.444205: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Mouse studies and in vivo infections: All 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).
    Euthanasia Agents: Flow cytometry analysis of immune cell infiltrates: For analysis of BAL fluid, mice were sacrificed by ketamine overdose, followed by cannulation of the trachea with a 19-G canula.
    Sex as a biological variableF2 mice (226 males, 177 females) were weaned such that littermates were randomized to different experimental cages to further reduce litter- or batch-effects on the study, and mice were transferred at 5-6 weeks of age to the RSB laboratory for infection between 9-12 weeks of age.
    RandomizationF2 mice (226 males, 177 females) were weaned such that littermates were randomized to different experimental cages to further reduce litter- or batch-effects on the study, and mice were transferred at 5-6 weeks of age to the RSB laboratory for infection between 9-12 weeks of age.
    BlindingFor 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 Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    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-CD11b
    anti-CD45
    suggested: (BD Biosciences Cat# 740809, RRID:AB_2740472)
    BV711
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    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 XXX), followed by agarose overlay.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Experimental Models: Organisms/Strains
    SentencesResources
    15- week old CCR9-/- mice (strain 027041) and 15-week old female C57BL/6NJ mice (strain 005304) were purchased from Jackson Laboratory.
    CCR9-/-
    suggested: None
    , CC-F2 mice, Trim14-deficient, and CCR9-/- mice were infected with 5×103 (CC-RIX with SARS-MA), 1×104 (CC-F2 with SARS-MA and SARS-CoV-2 MA10), and 1×105 (CC-RIX with HKU3-MA, Trim14Δ47/Δ47 and CCR9-/- mice with SARS-MA and SARS-CoV-2 MA10) plaque forming units (PFU) in 50 μl PBS intranasally at 9-12 (CC-RIX and CC-F2 mice) or 15 (CCR9-/- and C57BL/6NJ) weeks of age, respectively.
    C57BL/6NJ
    suggested: RRID:IMSR_JAX:005304)
    The sgRNA was mixed and co-injected with Cas9 RNA at 5ng/μl and 10ng/μl final concentrations into half-day-old C57BL/6J embryos (E0.5).
    C57BL/6J
    suggested: RRID:IMSR_JAX:000664)
    Trim14Δ47/Δ47 mice were born in normal Mendelian frequencies and showed no apparent defects in development, growth, or fecundity.
    Trim14Δ47/Δ47
    suggested: None
    Software and Algorithms
    SentencesResources
    Flow cytometric data were acquired on a cytometer (BD-X20; BD Biosciences) and analyzed using FlowJo software (Tree Star) (Figure S7).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    For the F2 crosses, instead of a regression on haplotype probabilities, the R/QTL package conducts a regression of the trait of interest on the exact genotypes at each locus54.
    R/QTL
    suggested: (R/QTL, RRID:SCR_009085)

    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).

    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.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.05.14.444205v1 on bioRxiv