SARS-CoV-2 infection is effectively treated and prevented by EIDD-2801.

Angela Wahl, Lisa E Gralinski, Claire E Johnson, Wenbo Yao, Martina Kovarova, Kenneth H Dinnon, Hongwei Liu, Victoria J Madden, Halina M Krzystek, Chandrav De, Kristen K White, Kendra Gully, Alexandra Schäfer, Tanzila Zaman, Sarah R Leist, Paul O Grant, Gregory R Bluemling, Alexander A Kolykhalov, Michael G Natchus, Frederic B Askin, George Painter, Edward P Browne, Corbin D Jones, Raymond J Pickles, Ralph S Baric, J Victor Garcia
Author Information
  1. Angela Wahl: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  2. Lisa E Gralinski: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  3. Claire E Johnson: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  4. Wenbo Yao: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  5. Martina Kovarova: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  6. Kenneth H Dinnon: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  7. Hongwei Liu: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  8. Victoria J Madden: Microscopy Services Laboratory, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  9. Halina M Krzystek: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  10. Chandrav De: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  11. Kristen K White: Microscopy Services Laboratory, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  12. Kendra Gully: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  13. Alexandra Schäfer: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  14. Tanzila Zaman: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  15. Sarah R Leist: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  16. Paul O Grant: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  17. Gregory R Bluemling: Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA. ORCID
  18. Alexander A Kolykhalov: Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA.
  19. Michael G Natchus: Drug Innovation Ventures at Emory (DRIVE), Atlanta, GA, USA.
  20. Frederic B Askin: Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  21. George Painter: Emory Institute of Drug Development (EIDD), Emory University, Atlanta, GA, USA.
  22. Edward P Browne: Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  23. Corbin D Jones: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  24. Raymond J Pickles: Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
  25. Ralph S Baric: Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ORCID
  26. J Victor Garcia: International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. victor_garcia@med.unc.edu. ORCID

Abstract

All coronaviruses known to have recently emerged as human pathogens probably originated in bats. Here we use a single experimental platform based on immunodeficient mice implanted with human lung tissue (hereafter, human lung-only mice (LoM)) to demonstrate the efficient in vivo replication of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as two endogenous SARS-like bat coronaviruses that show potential for emergence as human pathogens. Virus replication in this model occurs in bona fide human lung tissue and does not require any type of adaptation of the virus or the host. Our results indicate that bats contain endogenous coronaviruses that are capable of direct transmission to humans. Our detailed analysis of in vivo infection with SARS-CoV-2 in human lung tissue from LoM showed a predominant infection of human lung epithelial cells, including type-2 pneumocytes that are present in alveoli and ciliated airway cells. Acute infection with SARS-CoV-2 was highly cytopathic and induced a robust and sustained type-I interferon and inflammatory cytokine and chemokine response. Finally, we evaluated a therapeutic and pre-exposure prophylaxis strategy for SARS-CoV-2 infection. Our results show that therapeutic and prophylactic administration of EIDD-2801-an oral broad-spectrum antiviral agent that is currently in phase II/III clinical trials-markedly inhibited SARS-CoV-2 replication in vivo, and thus has considerable potential for the prevention and treatment of COVID-19.

References

  1. Cui, J., Li, F. & Shi, Z. L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 17, 181–192 (2019). [PMID: 30531947]
  2. Dong, E., Du, H. & Gardner, L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect. Dis. 20, 533–534 (2020). [PMID: 32087114]
  3. Boni, M. F. et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nat. Microbiol. 5, 1408–1417 (2020). [PMID: 32724171]
  4. Bao, L. et al. The pathogenicity of SARS-CoV-2 in hACE2 transgenic mice. Nature 583, 830–833 (2020). [PMID: 32380511]
  5. Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036–1045 (2020). [PMID: 32416070]
  6. Cockrell, A. S. et al. A mouse model for MERS coronavirus-induced acute respiratory distress syndrome. Nat. Microbiol. 2, 16226 (2017). [DOI: 10.1038/nmicrobiol.2016.226]
  7. Dinnon, K. H. III et al. A mouse-adapted model of SARS-CoV-2 to test COVID-19 countermeasures. Nature 586, 560–566 (2020). [PMID: 32854108]
  8. Gralinski, L. E. et al. Complement activation contributes to severe acute respiratory syndrome coronavirus pathogenesis. MBio 9, e01753-18 (2018). [PMID: 30301856]
  9. Jiang, R. D. et al. Pathogenesis of SARS-CoV-2 in transgenic mice expressing human angiotensin-converting enzyme 2. Cell 182, 50–58.e8 (2020). [PMID: 32516571]
  10. McCray, P. B. Jr et al. Lethal infection of K18-hACE2 mice infected with severe acute respiratory syndrome coronavirus. J. Virol. 81, 813–821 (2007). [PMID: 17079315]
  11. Menachery, V. D. et al. Middle East respiratory syndrome coronavirus nonstructural protein 16 is necessary for interferon resistance and viral pathogenesis. MSphere 2, e00346-17 (2017). [PMID: 29152578]
  12. Menachery, V. D. et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat. Med. 21, 1508–1513 (2015). [PMID: 26552008]
  13. Menachery, V. D. et al. SARS-like WIV1-CoV poised for human emergence. Proc. Natl Acad. Sci. USA 113, 3048–3053 (2016). [PMID: 26976607]
  14. Rockx, B. et al. Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model. Science 368, 1012–1015 (2020). [PMID: 32303590]
  15. Sheahan, T. P. et al. An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice. Sci. Transl. Med. 12, eabb5883 (2020). [PMID: 32253226]
  16. Franks, T. J. et al. Resident cellular components of the human lung: current knowledge and goals for research on cell phenotyping and function. Proc. Am. Thorac. Soc. 5, 763–766 (2008). [PMID: 18757314]
  17. Wahl, A. et al. Precision mouse models with expanded tropism for human pathogens. Nat. Biotechnol. 37, 1163–1173 (2019). [PMID: 31451733]
  18. Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280 (2020). [PMID: 32142651]
  19. Li, W. et al. Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature 426, 450–454 (2003). [PMID: 14647384]
  20. Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281–292 (2020). [PMID: 32155444]
  21. Yan, R. et al. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 367, 1444–1448 (2020). [PMID: 32132184]
  22. Carsana, L. et al. Pulmonary post-mortem findings in a series of COVID-19 cases from northern Italy: a two-centre descriptive study. Lancet Infect. Dis. 20, 1135–1140 (2020). [PMID: 32526193]
  23. Menter, T. et al. Postmortem examination of COVID-19 patients reveals diffuse alveolar damage with severe capillary congestion and variegated findings in lungs and other organs suggesting vascular dysfunction. Histopathology 77, 198–209 (2020). [PMID: 32364264]
  24. Tian, S. et al. Pulmonary pathology of early-phase 2019 novel coronavirus (COVID-19) pneumonia in two patients with lung cancer. J. Thorac. Oncol. 15, 700–704 (2020). [PMID: 32114094]
  25. Zhu, N. et al. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733 (2020). [PMID: 31978945]
  26. Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914–921 (2020). [PMID: 32330414]
  27. Merck Sharp & Dohme Corp. Efficacy and Safety of Molnupiravir (MK-4482) in Hospitalized Adult Participants With COVID-19 (MK-4482–001), https://ClinicalTrials.gov/show/NCT04575584 (2020).
  28. Xu, Z. et al. Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir. Med. 8, 420–422 (2020). [PMID: 32085846]
  29. Zhang, H. et al. Histopathologic changes and SARS-CoV-2 immunostaining in the lung of a patient with COVID-19. Ann. Intern. Med. 172, 629–632 (2020). [PMID: 32163542]
  30. Zhou, Z. et al. Heightened innate immune responses in the respiratory tract of COVID-19 patients. Cell Host Microbe 27, 883–890 (2020). [PMID: 32407669]
  31. Siu, K. L. et al. Severe acute respiratory syndrome coronavirus M protein inhibits type I interferon production by impeding the formation of TRAF3.TANK.TBK1/IKKε complex. J. Biol. Chem. 284, 16202–16209 (2009). [PMID: 19380580]
  32. Spiegel, M. et al. Inhibition of beta interferon induction by severe acute respiratory syndrome coronavirus suggests a two-step model for activation of interferon regulatory factor 3. J. Virol. 79, 2079–2086 (2005). [PMID: 15681410]
  33. Vanderheiden, A. et al. Type I and type III interferons restrict SARS-CoV-2 infection of human airway epithelial cultures. J. Virol. 94, e00985-20 (2020). [PMID: 32699094]
  34. Qin, C. et al. Dysregulation of immune response in patients with coronavirus 2019 (COVID-19) in Wuhan, China. Clin. Infect. Dis. 71, 762–768 (2020). [PMID: 32161940]
  35. Beigel, J. H. et al. Remdesivir for the treatment of Covid-19 – final report. N. Engl. J. Med. 383, 1813–1826 (2020). [PMID: 32445440]
  36. WHO Solidarity Trial Consortium. Repurposed antiviral drugs for COVID-19 –interim WHO Solidarity trial results. N. Engl. J. Med. 384, 497–511 (2021). [DOI: 10.1056/NEJMoa2023184]
  37. Chen, P. et al. SARS-CoV-2 neutralizing antibody LY-CoV555 in outpatients with Covid-19. N. Engl. J. Med. 384, 229–237 (2021). [PMID: 33113295]
  38. Regeneron Pharmaceuticals Inc. Regeneron’s COVID-19 outpatient trial prospectively demonstrates that REGN-COV2 antibody cocktail significantly reduced virus levels and need for further medical attention. https://newsroom.regeneron.com/news-releases/news-release-details/regenerons-covid-19-outpatient-trial-prospectively-demonstrates (2020).
  39. Kim, P. S., Read, S. W. & Fauci, A. S. Therapy for early COVID-19: a critical need. J. Am. Med. Assoc. 324, 2149–2150 (2020). [DOI: 10.1001/jama.2020.22813]
  40. Sticher, Z. M. et al. Analysis of the potential for N-hydroxycytidine to inhibit mitochondrial replication and function. Antimicrob. Agents Chemother. 64, e01719-19 (2020). [PMID: 31767721]
  41. Toots, M. et al. Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia. Sci. Transl. Med. 11, eaax5866 (2019). [PMID: 31645453]
  42. Cox, R. M., Wolf, J. D. & Plemper, R. K. Therapeutically administered ribonucleoside analogue MK-4482/EIDD-2801 blocks SARS-Cov-2 transmission in ferrets. Nat. Microbiol. 6, 11–18 (2021). [PMID: 33273742]
  43. Hou, Y. J. et al. SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract. Cell 182, 429–446 (2020). [PMID: 32526206]
  44. Scobey, T. et al. Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus. Proc. Natl Acad. Sci. USA 110, 16157–16162 (2013). [PMID: 24043791]
  45. Yount, B. et al. Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus. Proc. Natl Acad. Sci. USA 100, 12995–13000 (2003). [PMID: 14569023]
  46. Simionescu, N. & Simionescu, M. Galloylglucoses of low molecular weight as mordant in electron microscopy. I. Procedure, and evidence for mordanting effect. J. Cell Biol. 70, 608–621 (1976). [PMID: 783172]
  47. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013). [DOI: 10.1093/bioinformatics/bts635]
  48. Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods 14, 417–419 (2017). [PMID: 28263959]
  49. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014). [PMID: 25516281]
  50. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289–300, (1995).
  51. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005). [PMID: 16199517]
  52. Eden, E., Navon, R., Steinfeld, I., Lipson, D. & Yakhini, Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10, 48 (2009). [PMID: 19192299]

Grants

  1. R21 AI113736/NIAID NIH HHS
  2. R01 MH108179/NIMH NIH HHS
  3. R01 AI123010/NIAID NIH HHS
  4. R01 AI108197/NIAID NIH HHS
  5. P30 CA016086/NCI NIH HHS
  6. R01 AI140799/NIAID NIH HHS
  7. R21 AI138247/NIAID NIH HHS
  8. R01 AI111899/NIAID NIH HHS
  9. U19 AI100625/NIAID NIH HHS

MeSH Term

Administration, Oral
Alveolar Epithelial Cells
Animals
COVID-19
Chemoprevention
Chiroptera
Clinical Trials, Phase II as Topic
Clinical Trials, Phase III as Topic
Cytidine
Cytokines
Epithelial Cells
Female
Heterografts
Humans
Hydroxylamines
Immunity, Innate
Interferon Type I
Lung
Lung Transplantation
Male
Mice
Post-Exposure Prophylaxis
Pre-Exposure Prophylaxis
SARS-CoV-2
Virus Replication
COVID-19 Drug Treatment

Chemicals

Cytokines
Hydroxylamines
Interferon Type I
Cytidine
molnupiravir