A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs.

Nanda Kishore Routhu, Narayanaiah Cheedarla, Sailaja Gangadhara, Venkata Satish Bollimpelli, Arun K Boddapati, Ayalnesh Shiferaw, Sheikh Abdul Rahman, Anusmita Sahoo, Venkata Viswanadh Edara, Lilin Lai, Katharine Floyd, Shelly Wang, Stephanie Fischinger, Caroline Atyeo, Sally A Shin, Sanjeev Gumber, Shannon Kirejczyk, Joyce Cohen, Sherrie M Jean, Jennifer S Wood, Fawn Connor-Stroud, Rachelle L Stammen, Amit A Upadhyay, Kathryn Pellegrini, David Montefiori, Pei-Yong Shi, Vineet D Menachery, Galit Alter, Thomas H Vanderford, Steven E Bosinger, Mehul S Suthar, Rama Rao Amara
Author Information
  1. Nanda Kishore Routhu: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  2. Narayanaiah Cheedarla: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  3. Sailaja Gangadhara: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  4. Venkata Satish Bollimpelli: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  5. Arun K Boddapati: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  6. Ayalnesh Shiferaw: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  7. Sheikh Abdul Rahman: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  8. Anusmita Sahoo: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  9. Venkata Viswanadh Edara: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA.
  10. Lilin Lai: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA.
  11. Katharine Floyd: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA.
  12. Shelly Wang: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  13. Stephanie Fischinger: Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  14. Caroline Atyeo: Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  15. Sally A Shin: Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  16. Sanjeev Gumber: Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  17. Shannon Kirejczyk: Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  18. Joyce Cohen: Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
  19. Sherrie M Jean: Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
  20. Jennifer S Wood: Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
  21. Fawn Connor-Stroud: Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
  22. Rachelle L Stammen: Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
  23. Amit A Upadhyay: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  24. Kathryn Pellegrini: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  25. David Montefiori: Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA.
  26. Pei-Yong Shi: Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
  27. Vineet D Menachery: Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA.
  28. Galit Alter: Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
  29. Thomas H Vanderford: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
  30. Steven E Bosinger: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
  31. Mehul S Suthar: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA.
  32. Rama Rao Amara: Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA. Electronic address: ramara@emory.edu.

Abstract

A combination of vaccination approaches will likely be necessary to fully control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Here, we show that modified vaccinia Ankara (MVA) vectors expressing membrane-anchored pre-fusion stabilized spike (MVA/S) but not secreted S1 induced strong neutralizing antibody responses against SARS-CoV-2 in mice. In macaques, the MVA/S vaccination induced strong neutralizing antibodies and CD8 T cell responses, and conferred protection from SARS-CoV-2 infection and virus replication in the lungs as early as day 2 following intranasal and intratracheal challenge. Single-cell RNA sequencing analysis of lung cells on day 4 after infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities and lowered induction of interferon-stimulated genes. These results demonstrate that MVA/S vaccination induces neutralizing antibodies and CD8 T cells in the blood and lungs and is a potential vaccine candidate for SARS-CoV-2.

Keywords

References

  1. Science. 2020 Mar 13;367(6483):1260-1263 [PMID: 32075877]
  2. Cell. 2020 Nov 25;183(5):1367-1382.e17 [PMID: 33160446]
  3. Cell. 2020 Aug 20;182(4):812-827.e19 [PMID: 32697968]
  4. J Immunol Methods. 2011 Mar 7;366(1-2):8-19 [PMID: 21192942]
  5. J Immunol. 2015 Nov 15;195(10):5025-34 [PMID: 26482408]
  6. J Immunol Methods. 2019 Aug;471:46-56 [PMID: 31132351]
  7. Nat Med. 2020 Nov;26(11):1694-1700 [PMID: 32884153]
  8. Nat Med. 2004 Sep;10(9):927-34 [PMID: 15311275]
  9. Nature. 2020 Sep;585(7824):268-272 [PMID: 32396922]
  10. PLoS One. 2016 Oct 6;11(10):e0163164 [PMID: 27711228]
  11. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):E7348-E7357 [PMID: 28807998]
  12. Virology. 2007 Sep 15;366(1):73-83 [PMID: 17507071]
  13. Nat Immunol. 2019 Feb;20(2):163-172 [PMID: 30643263]
  14. Cell Rep Med. 2020 Jun 23;1(3):100040 [PMID: 32835303]
  15. Clin Microbiol Rev. 2015 Apr;28(2):465-522 [PMID: 25810418]
  16. Vaccines (Basel). 2014 Feb 28;2(1):160-78 [PMID: 26344473]
  17. Nature. 2020 Oct;586(7830):578-582 [PMID: 32731258]
  18. N Engl J Med. 2020 Oct 15;383(16):1544-1555 [PMID: 32722908]
  19. Cell. 2021 Jan 21;184(2):460-475.e21 [PMID: 33278358]
  20. Cell. 2021 Mar 4;184(5):1188-1200.e19 [PMID: 33577765]
  21. PLoS Negl Trop Dis. 2018 Oct 24;12(10):e0006862 [PMID: 30356267]
  22. Nature. 2020 Oct;586(7830):594-599 [PMID: 32998157]
  23. Nat Med. 2020 Jun;26(6):842-844 [PMID: 32398875]
  24. Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205 [PMID: 31114916]
  25. J Virol. 2002 Aug;76(15):7625-31 [PMID: 12097576]
  26. Emerg Infect Dis. 2020 Jul;26(7):1633-1635 [PMID: 32294051]
  27. Science. 2001 Apr 6;292(5514):69-74 [PMID: 11393868]
  28. Sci Transl Med. 2021 Jan 27;13(578): [PMID: 33431511]
  29. J Virol. 2019 Feb 19;93(5): [PMID: 30541829]
  30. J Immunol. 2016 Nov 1;197(9):3586-3596 [PMID: 27683750]
  31. Cell. 2020 Nov 25;183(5):1354-1366.e13 [PMID: 33065030]
  32. Science. 2020 Jul 3;369(6499):77-81 [PMID: 32376603]
  33. Nature. 2012 Jan 04;482(7383):89-93 [PMID: 22217938]
  34. J Infect Dis. 2014 Jul 1;210(1):99-110 [PMID: 24403557]
  35. Sci Rep. 2018 Jan 16;8(1):864 [PMID: 29339750]
  36. Nature. 2020 May;581(7809):465-469 [PMID: 32235945]
  37. J Immunol Methods. 2017 Apr;443:33-44 [PMID: 28163018]
  38. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W741-8 [PMID: 15980575]
  39. PLoS Pathog. 2020 Sep 18;16(9):e1008903 [PMID: 32946524]
  40. Immunity. 2020 Oct 13;53(4):724-732.e7 [PMID: 32783919]
  41. Sci Rep. 2017 Nov 7;7(1):14769 [PMID: 29116169]
  42. Science. 1996 Apr 12;272(5259):263-7 [PMID: 8602510]
  43. Semin Immunol. 2004 Jun;16(3):163-70 [PMID: 15130500]
  44. Nat Med. 2005 Apr;11(4 Suppl):S25-32 [PMID: 15812486]
  45. J Clin Invest. 2010 Nov;120(11):3878-90 [PMID: 20972331]
  46. Nat Biotechnol. 2018 Jun;36(5):411-420 [PMID: 29608179]
  47. Front Microbiol. 2019 Aug 02;10:1781 [PMID: 31428074]
  48. Cell Host Microbe. 2020 May 13;27(5):841-848.e3 [PMID: 32289263]
  49. N Engl J Med. 2020 Dec 10;383(24):2320-2332 [PMID: 32877576]
  50. Nature. 2020 Oct;586(7830):583-588 [PMID: 32731257]
  51. Nat Commun. 2020 May 20;11(1):2601 [PMID: 32433465]
  52. Expert Rev Vaccines. 2017 Oct;16(10):973-985 [PMID: 28838267]
  53. J Infect Dis. 2011 Mar 1;203(5):610-9 [PMID: 21282192]
  54. N Engl J Med. 2016 Apr 28;374(17):1635-46 [PMID: 25629663]
  55. Emerg Microbes Infect. 2019;8(1):841-856 [PMID: 31169078]
  56. Nature. 2020 Oct;586(7830):516-527 [PMID: 32967006]
  57. Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6641-6 [PMID: 15096611]
  58. Cell. 2019 Jun 13;177(7):1888-1902.e21 [PMID: 31178118]
  59. Science. 2020 Aug 14;369(6505):806-811 [PMID: 32434945]
  60. J Immunol Methods. 2012 Dec 14;386(1-2):117-23 [PMID: 23023091]
  61. PLoS One. 2009 Sep 23;4(9):e7142 [PMID: 19774076]
  62. Science. 2016 Jan 1;351(6268):77-81 [PMID: 26678878]
  63. J Immunol Methods. 2019 Oct;473:112630 [PMID: 31301278]
  64. Lancet. 2020 Nov 14;396(10262):1595-1606 [PMID: 33065034]
  65. Vaccine. 2013 Sep 6;31(39):4241-6 [PMID: 23523410]
  66. AIDS Res Hum Retroviruses. 2004 Jun;20(6):645-53 [PMID: 15242542]

Grants

  1. HHSN272201400008C/NIAID NIH HHS
  2. P51 OD011132/NIH HHS
  3. R01 AI148378/NIAID NIH HHS
  4. S10 OD026799/NIH HHS

MeSH Term

Animals
Antibodies, Neutralizing
Antibodies, Viral
Antigens, Viral
COVID-19
COVID-19 Vaccines
Disease Models, Animal
Gene Expression
Gene Order
Genetic Vectors
Immunophenotyping
Lung
Macaca
Macrophages, Alveolar
Mice
SARS-CoV-2
Spike Glycoprotein, Coronavirus
T-Lymphocyte Subsets
Vaccination
Vaccines, DNA
Vaccinia virus

Chemicals

Antibodies, Neutralizing
Antibodies, Viral
Antigens, Viral
COVID-19 Vaccines
Spike Glycoprotein, Coronavirus
Vaccines, DNA
spike protein, SARS-CoV-2