. 2022 Oct 23;13(1):6309.

doi: 10.1038/s41467-022-33985-4.

Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Dapeng Li^{1

2}, David R Martinez³, Alexandra Schäfer³, Haiyan Chen^{1

2}, Maggie Barr¹, Laura L Sutherland¹, Esther Lee^{1

2}, Robert Parks¹, Dieter Mielke⁴, Whitney Edwards¹, Amanda Newman^{1

2}, Kevin W Bock⁵, Mahnaz Minai⁵, Bianca M Nagata⁵, Matthew Gagne⁶, Daniel C Douek⁶, C Todd DeMarco^{1

2}, Thomas N Denny^{1

2}, Thomas H Oguin 3rd^{1

2}, Alecia Brown^{1

2}, Wes Rountree^{1

2}, Yunfei Wang^{1

2}, Katayoun Mansouri¹, Robert J Edwards^{1

2}, Guido Ferrari^{1

4}, Gregory D Sempowski^{1

2}, Amanda Eaton^{1

4}, Juanjie Tang⁷, Derek W Cain^{1

2}, Sampa Santra⁸, Norbert Pardi⁹, Drew Weissman¹⁰, Mark A Tomai¹¹, Christopher B Fox¹², Ian N Moore⁵, Hanne Andersen¹³, Mark G Lewis¹³, Hana Golding⁷, Robert Seder⁶, Surender Khurana⁷, Ralph S Baric³, David C Montefiori^{1

4}, Kevin O Saunders^{14

15

16

17}, Barton F Haynes^{18

19

20}

Affiliations

¹ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
² Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
³ Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
⁴ Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA.
⁵ Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
⁶ Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
⁷ Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD, 20871, USA.
⁸ Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
⁹ Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
¹⁰ Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
¹¹ Corporate Research Materials Lab, 3M Company, St Paul, MN, 55144, USA.
¹² Infectious Disease Research Institute, Seattle, WA, 98104, USA.
¹³ BIOQUAL, Rockville, MD, 20850, USA.
¹⁴ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁵ Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁶ Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁷ Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁸ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.
¹⁹ Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.
²⁰ Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.

PMID: 36274085
PMCID: PMC9588772
DOI: 10.1038/s41467-022-33985-4

Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Dapeng Li et al. Nat Commun. 2022.

. 2022 Oct 23;13(1):6309.

doi: 10.1038/s41467-022-33985-4.

Authors

Affiliations

¹ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
² Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
³ Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
⁴ Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA.
⁵ Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
⁶ Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
⁷ Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration, Silver Spring, MD, 20871, USA.
⁸ Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
⁹ Department of Microbiology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
¹⁰ Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
¹¹ Corporate Research Materials Lab, 3M Company, St Paul, MN, 55144, USA.
¹² Infectious Disease Research Institute, Seattle, WA, 98104, USA.
¹³ BIOQUAL, Rockville, MD, 20850, USA.
¹⁴ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁵ Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁶ Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁷ Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, 27710, USA. kevin.saunders@duke.edu.
¹⁸ Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.
¹⁹ Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.
²⁰ Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA. barton.haynes@duke.edu.

PMID: 36274085
PMCID: PMC9588772
DOI: 10.1038/s41467-022-33985-4

Abstract

Coronavirus vaccines that are highly effective against current and anticipated SARS-CoV-2 variants are needed to control COVID-19. We previously reported a receptor-binding domain (RBD)-sortase A-conjugated ferritin nanoparticle (scNP) vaccine that induced neutralizing antibodies against SARS-CoV-2 and pre-emergent sarbecoviruses and protected non-human primates (NHPs) from SARS-CoV-2 WA-1 infection. Here, we find the RBD-scNP induced neutralizing antibodies in NHPs against pseudoviruses of SARS-CoV and SARS-CoV-2 variants including 614G, Beta, Delta, Omicron BA.1, BA.2, BA.2.12.1, and BA.4/BA.5, and a designed variant with escape mutations, PMS20. Adjuvant studies demonstrate variant neutralization titers are highest with 3M-052-aqueous formulation (AF). Immunization twice with RBD-scNPs protect NHPs from SARS-CoV-2 WA-1, Beta, and Delta variant challenge, and protect mice from challenges of SARS-CoV-2 Beta variant and two other heterologous sarbecoviruses. These results demonstrate the ability of RBD-scNPs to induce broad neutralization of SARS-CoV-2 variants and to protect animals from multiple different SARS-related viruses. Such a vaccine could provide broad immunity to SARS-CoV-2 variants.

PubMed Disclaimer

Conflict of interest statement

B.F.H. and K.O.S. have filed US patents regarding the nanoparticle vaccine, M.A.T. and the 3M company have US patents filed on 3M-052, and C.B.F. and IDRI have filed a patent on the formulation of 3M-052-AF and 3M-052-Alum. The 3M company had no role in the execution of the study, data collection or data interpretation. D.W. is named on US patents that describe the use of nucleoside-modified mRNA as a platform to deliver therapeutic proteins. D.W. and N.P. are also named on a US patent describing the use of nucleoside-modified mRNA in lipid nanoparticles as a vaccine platform. All other authors declare no competing interests.

Figures

**Fig. 1. Neutralizing antibodies and in vivo protection elicited by RBD-scNP vaccine formulated with three different adjuvants.**
a Schematic of the vaccination and challenge study. Cynomolgus macaques (n = 5 per group) were immunized intramuscularly 3 times with 100 μg of RBD-scNP adjuvanted with 3M-052-Alum, Alum, 3M052-AF, or PBS control. Animals injected with adjuvant alone or PBS were set as control groups. Monkeys were then challenged with SARS-CoV-2 WA-1, subjected to blood, Bronchoalveolar lavage (BAL) and nasal swab collection, and necropsied for pathologic analysis. b Neutralization titers (ID₅₀) of plasma antibodies against pseudovirus of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns, not significant, *p < 0.05, two-sided Wilcoxon rank sum exact test. c Serum antibody neutralization against pseudoviruses of the SARS-CoV-2 Omicron (BA.1, BA.2, BA.2.12.1, BA.4/BA.5) variants, and SARS-CoV-2 PMS20 variant in 293T-ACE2 cells. The geometric mean titers and the fold reduction compared to D614G are shown. d Serum antibody neutralization against pseudoviruses of SARS-CoV in 293T-ACE2 cells. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns, not significant, *p < 0.05, two-sided Wilcoxon rank sum exact test. e SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Dashed line indicates limit of the detection. f, g Histopathological analysis. Lung sections from each animal were scored for lung inflammation by haematoxylin and eosin (H&E) staining (f), and for SARS-CoV-2 nucleocapsid antigen (Ag) expression by immunohistochemistry (IHC) staining (g). Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns not significant, *p < 0.05, two-sided Wilcoxon rank sum exact test. Source data are provided as a Source Data file.

**Fig. 2. Neutralizing antibodies and in vivo protection induced by RBD-scNP, NTD-scNP and S2P-scNP vaccines.**
a Negative-stain electron microscopy 2D class averaging of RBD-scNP, NTD-scNP, and S2P-scNP. The 2D class averaging of 14,300 RBD-scNP particles, 10,800 NTD-scNP particles or 1034 S2P-scNP particles were generated using RELION. The size of each box: RBD-scNP and NTD-scNP, 257 Å; S2P-scNP, 1029 Å. b Schematic of the three-dose regimen. Cynomolgus macaques (n = 5 per group) were immunized 3 times with RBD-scNP, NTD-scNP, or S2P-scNP adjuvanted with 3M-052-Alum. Monkeys were then challenged with SARS-CoV-2 WA-1, sampled for blood, BAL and nasal swabs, and necropsied for pathologic analysis. c Neutralization titers of plasma antibodies (week 0, 2, 6 and 10) against pseudotyped SARS-CoV-2 D614G strain in 293T/ACE2.MF cells. d Neutralization titers of plasma antibodies (week 10) against live SARS-CoV-2 WA-1 virus in Vero-E6 cells in microneutralization (MN) assay. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns not significant, *p < 0.05, two-sided Wilcoxon rank sum exact test. e Neutralization titers of plasma antibodies (n = 5 per group) against pseudoviruses of the SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns, not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. f, g Serum antibody neutralization against pseudoviruses of (f) the SARS-CoV-2 Omicron BA.1 and BA.2 variants, the PMS20 variant, and (g) SARS-CoV in 293T-ACE2 cells. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. For SARS-CoV-2, the geometric mean titers and the fold reduction compared to D614G are shown. Adjusted p-values: ns, not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. h SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. i, j Histopathological analysis. Scores of lung inflammation were determined by H&E staining (i) and SARS-CoV-2 nucleocapsid antigen expression were determined by IHC staining (j). Source data are provided as a Source Data file.

**Fig. 3. RBD-scNP, NTD-scNP and S2P-scNP vaccines as a heterologous boost for the S2P mRNA-LNP vaccine.**
a Schematic of the heterologous prime-boost regimen. Cynomolgus macaques (n = 5 per group) were immunized 2 times with S2P mRNA-LNP, and boosted with adjuvanted RBD-scNP, NTD-scNP, or S2P-scNP vaccine. Monkeys were then challenged with SARS-CoV-2 WA-1, sampleded for blood, BAL and nasal swabs, and necropsied for pathologic analysis. b Neutralization titers of plasma antibodies against pseudoviruses of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. Serum antibody neutralization titers against pseudoviruses of (c) the SARS-CoV-2 Omicron BA.1 and BA.2 variants, (d) the SARS-CoV-2 PMS20 variant, and (e) SARS-CoV in 293T-ACE2 cells. Each dot indicates one monkey (n = 5 per group) and bars indicate geometric mean values of each group. For SARS-CoV-2, the geometric mean titers and the fold reduction compared to D614G are shown. Adjusted p-values: ns not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. f SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. Histopathological analysis. Scores of lung inflammation were determined by H&E staining (g) and SARS-CoV-2 nucleocapsid antigen expression were determined by IHC staining (h). Source data are provided as a Source Data file.

**Fig. 4. Two doses of RBD-scNP vaccination protected non-human primates from challenges of SARS-CoV-2 variants.**
a Schematic of the vaccination and challenge studies. Cynomolgus macaques were immunized twice with RBD-scNP adjuvanted with 3M-052-Alum, and challenged with SARS-CoV-2 WA-1 strain (n = 5) or B.1.351 (Beta; n = 5) or B.1.617.2 (Delta; n = 5), collected for blood, BAL and nasal swab samples, and necropsied for pathologic analysis. b Neutralization titers of plasma antibodies against pseudoviruses of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. Each dot indicates one monkey (n = 10 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. Neutralization titers of serum antibodies against pseudoviruses of (c) the SARS-CoV-2 Omicron BA.1 and BA.2 variants, (d) the SARS-CoV-2 PMS20 variant, and (e) SARS-CoV in 293T-ACE2 cells. Each dot indicates one monkey (n = 15 per group) and bars indicate geometric mean values of each group. Adjusted p-values: ns, not significant, *p < 0.05, Two-sided Wilcoxon rank sum exact test. For SARS-CoV-2 variants, the geometric mean ID₅₀ titers and the fold reduction compared to D614G are shown. SARS-CoV-2 sgRNA levels for nucleocapsid (N) gene in BAL and nasal swab samples collected on day 2 and 4 after (f) SARS-CoV-2 WA-1, (g) Beta variant or (h) Delta variant challenge. Dashed line indicates limit of the detection (LOD). Histopathological analysis of the SARS-CoV-2 (i) WA-1, (j) Beta variant or (k) Delta variant challenged monkeys. Scores of lung inflammation determined by H&E staining and SARS-CoV-2 nucleocapsid Ag expression determined by IHC staining. Source data are provided as a Source Data file.

**Fig. 5. Two doses of RBD-scNP vaccination protected mice from challenges of SARS-CoV-2 variants and other betacoronaviruses.**
a Schematic of the mouse challenge studies. 11-month-old female BALB/c mice (n = 10 per group) were immunized intramuscularly twice with adjuvanted RBD-scNP and challenged with SARS-CoV-2 mouse-adapted 10 (MA10) WA-1, SARS-CoV-2 MA10 Beta variant, SARS-CoV-1 mouse-adapted 15 (MA15), or Bat coronavirus (CoV) RsSHC014 MA15. GLA-SE was used as adjuvant in the SARS-CoV challenge study, and 3M-052-Alum was used in the other challenge studies. b Weight loss (n = 10 per group) and lung virus titers (n = 10 per group) at 4 days post-infection (dpi) of the SARS-CoV-2 MA10 WA-1 challenged mice. c Weight loss (n = 5 per group) and lung virus titers (n = 4 per group) at 2 dpi of the SARS-CoV-2 MA10 Beta variant challenged mice. d Weight loss (n = 10 per group) and lung virus titers (n = 5 per group) at 2 dpi of the SARS-CoV-1 MA15 challenged mice. e Weight loss (n = 10 per group) and lung virus titers (n = 10 per group) at 4 dpi of the Bat CoV RsSHC014 MA15 challenged mice. For weight curves, data are presented as mean values ±SEM. For lung virus titers, each dot indicates one mouse and bars indicate geometric mean values of each group. P-values: ns not significant, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, Two-sided Wilcoxon rank sum exact test. Source data are provided as a Source Data file.

See this image and copyright information in PMC

Update of

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine.
Li D, Martinez DR, Schäfer A, Chen H, Barr M, Sutherland LL, Lee E, Parks R, Mielke D, Edwards W, Newman A, Bock KW, Minai M, Nagata BM, Gagne M, Douek DC, DeMarco CT, Denny TN, Oguin TH 3rd, Brown A, Rountree W, Wang Y, Mansouri K, Edwards RJ, Ferrari G, Sempowski GD, Eaton A, Tang J, Cain DW, Santra S, Pardi N, Weissman D, Tomai MA, Fox CB, Moore IN, Andersen H, Lewis MG, Golding H, Seder R, Khurana S, Baric RS, Montefiori DC, Saunders KO, Haynes BF. Li D, et al. bioRxiv [Preprint]. 2022 Feb 14:2022.01.26.477915. doi: 10.1101/2022.01.26.477915. bioRxiv. 2022. Update in: Nat Commun. 2022 Oct 23;13(1):6309. doi: 10.1038/s41467-022-33985-4. PMID: 35118474 Free PMC article. Updated. Preprint.

References

1. Chaudhary N, Weissman D, Whitehead KA. mRNA vaccines for infectious diseases: principles, delivery and clinical translation. Nat. Rev. Drug Disco. 2021;20:817–838. doi: 10.1038/s41573-021-00283-5. - DOI - PMC - PubMed
1. Pardi N, Hogan MJ, Porter FW, Weissman D. mRNA vaccines—a new era in vaccinology. Nat. Rev. Drug Disco. 2018;17:261–279. doi: 10.1038/nrd.2017.243. - DOI - PMC - PubMed
1. Pardi N, Hogan MJ, Weissman D. Recent advances in mRNA vaccine technology. Curr. Opin. Immunol. 2020;65:14–20. doi: 10.1016/j.coi.2020.01.008. - DOI - PubMed
1. Baden LR, et al. Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N. Engl. J. Med. 2021;384:403–416. doi: 10.1056/NEJMoa2035389. - DOI - PMC - PubMed
1. Polack FP, et al. Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine. N. Engl. J. Med. 2020;383:2603–2615. doi: 10.1056/NEJMoa2034577. - DOI - PMC - PubMed

Publication types

Actions
Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions
Actions
Actions
Actions
Actions

Supplementary concepts

Actions

Grants and funding

LinkOut - more resources

Full Text Sources
Other Literature Sources
- The Lens - Patent Citations Database
Medical
- MedlinePlus Health Information
Research Materials
- Addgene Non-profit plasmid repository
Miscellaneous
- NCI CPTAC Assay Portal

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Affiliations

Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Update of

References

Publication types

MeSH terms

Substances

Supplementary concepts

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Research Materials

Miscellaneous