Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
[Preprint]. 2022 Feb 14:2022.01.26.477915.
doi: 10.1101/2022.01.26.477915.

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine

Dapeng Li  1   2 , David R Martinez  3 , Alexandra Schäfer  3 , Haiyan Chen  1   2 , Maggie Barr  1 , Laura L Sutherland  1 , Esther Lee  1   2 , Robert Parks  1 , Dieter Mielke  4 , Whitney Edwards  1 , Amanda Newman  1   2 , Kevin W Bock  5 , Mahnaz Minai  5 , Bianca M Nagata  5 , Matthew Gagne  6 , Daniel C Douek  6 , 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 Mansouri  1 , Robert J Edwards  1   2 , Guido Ferrari  4 , Gregory D Sempowski  1   2 , Amanda Eaton  1   4 , Juanjie Tang  7 , Derek W Cain  1   2 , Sampa Santra  8 , Norbert Pardi  9 , Drew Weissman  10 , Mark A Tomai  11 , Christopher B Fox  12 , Ian N Moore  5 , Hanne Andersen  13 , Mark G Lewis  13 , Hana Golding  7 , Robert Seder  6 , Surender Khurana  7 , Ralph S Baric  3 , David C Montefiori  1   4 , Kevin O Saunders  1   4   14   15 , Barton F Haynes  1   2   14
Affiliations

Breadth of SARS-CoV-2 Neutralization and Protection Induced by a Nanoparticle Vaccine

Dapeng Li et al. bioRxiv. .

Update in

  • 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. Nat Commun. 2022 Oct 23;13(1):6309. doi: 10.1038/s41467-022-33985-4. Nat Commun. 2022. PMID: 36274085 Free PMC article.

Abstract

Coronavirus vaccines that are highly effective against SARS-CoV-2 variants are needed to control the current pandemic. We previously reported a receptor-binding domain (RBD) sortase A-conjugated ferritin nanoparticle (RBD-scNP) vaccine that induced neutralizing antibodies against SARS-CoV-2 and pre-emergent sarbecoviruses and protected monkeys from SARS-CoV-2 WA-1 infection. Here, we demonstrate SARS-CoV-2 RBD-scNP immunization induces potent neutralizing antibodies in non-human primates (NHPs) against all eight SARS-CoV-2 variants tested including the Beta, Delta, and Omicron variants. The Omicron variant was neutralized by RBD-scNP-induced serum antibodies with a mean of 10.6-fold reduction of ID50 titers compared to SARS-CoV-2 D614G. Immunization with RBD-scNPs protected NHPs from SARS-CoV-2 WA-1, Beta, and Delta variant challenge, and protected 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 NHPs and mice from multiple different SARS-related viruses. Such a vaccine could provide the needed immunity to slow the spread of and reduce disease caused by SARS-CoV-2 variants such as Delta and Omicron.

PubMed Disclaimer

Conflict of interest statement

COMPETING FINANCIAL INTERESTS

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-AF + 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

Figure 1.
Figure 1.. RBD-scNP vaccination elicits broad neutralizing antibodies against SARS-CoV-2 variants in macaques.
(A) Schematic of the vaccination study. Cynomolgus macaques (n=5 per group) were immunized 3 times with PBS control or 100 μg RBD-scNP adjuvanted with 3M-052-AF + Alum. (B-C) Plasma antibody (post-3rd immunization) neutralization of SARS-CoV-2 variants pseudovirus infection in 293T-ACE2-TMPRSS2 cells. (B) Neutralization 50% inhibitory dilution (ID50) titers. Each symbol represents an individual macaque. Bars indicate group geometric mean ID50. (C) Reduction of ID50 titers against variants were shown as fold reduction compared to the titers against WA-1. Each row shows values for an individual macaque for each virus. (D) Plasma antibody (post-3rd immunization) neutralization titers against pseudoviruses of the SARS-CoV-2 Omicron variants in 293T-ACE2 cells. The geometric mean ID50 and ID80 titers and the fold reduction compared to D614G are shown.
Figure 2.
Figure 2.. Two doses of RBD-scNP vaccination protected non-human primates and mice from challenges of SARS-CoV-2 variants and other betacoronaviruses.
(A) Schematic of the vaccination and challenge studies. Cynomolgus macaques were immunized twice 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). Bronchoalveolar lavage (BAL) and nasal swab samples were collected for subgenomic (sgRNA) viral replication tests. Animals were necropsied on day 4 post-challenge for pathologic analysis. (B) Plasma antibody neutralization ID50 titers against pseudoviruses of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. (C) Plasma antibody neutralization ID50 titers against pseudoviruses of SARS-CoV-2 Omicron variants in 293T-ACE2 cells. The geometric mean ID50 and ID80 titers and the fold reduction compared to D614G are shown. (D-F) SARS-CoV-2 sgRNA levels for nucleocapsid (N) gene in BAL and nasal swab samples collected on day 2 and 4 after SARS-CoV-2 WA-1 (D), Beta variant (E) or Delta variant (F) challenge. Dashed line indicates limit of the detection (LOD). (G-H) Histopathological analysis of the SARS-CoV-2 WA-1 (G) and Beta variant (H) challenged monkeys. Scores of lung inflammation determined by haematoxylin and eosin (H&E) staining and SARS-CoV-2 nucleocapsid antigen (Ag) expression determined by immunohistochemistry (IHC) staining. (I) Schematic of the mouse challenge studies. Aged female BALB/c mice (n=10 per group) were immunized intramuscularly twice 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. (J) Weight loss and lung virus titers at 4 days post-infection (dpi) of the SARS-CoV-2 MA10 WA-1 challenged mice. (K) Weight loss and lung virus titers at 2 dpi of the SARS-CoV-2 MA10 Beta variant challenged mice. (L) Weight loss and lung virus titers at 2 dpi of the SARS-CoV-1 MA15 challenged mice. (M) Weight loss and lung virus titers at 4 dpi of the Bat CoV RsSHC014 MA15 challenged mice. ns, not significant, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001, Wilcoxon rank sum exact test.
Figure 3.
Figure 3.. 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 3M052-AF + 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, collected for blood, BAL and nasal swab samples, and necropsied for pathologic analysis. (B) Neutralization ID50 titers of plasma antibodies (post-3rd immunization) against pseudovirus of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2. (C) Plasma antibody (post-2nd and post-3rd immunization) neutralization titers against pseudoviruses of the SARS-CoV-2 Omicron variants in 293T-ACE2 cells. The geometric mean ID50 titers and the fold reduction compared to D614G are shown. The dashed arrows indicate fold increase of ID50 titer induced by the 3rd boost. (D) SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. Dashed line indicates limit of the detection. (E) Histopathological analysis. Lung sections from each animal were scored for lung inflammation by H&E staining, and for SARS-CoV-2 nucleocapsid Ag expression by IHC staining. ns, not significant, *P<0.05, Wilcoxon rank sum exact test.
Figure 4.
Figure 4.. Neutralizing antibodies and in vivo protection induced by RBD-scNP, NTD-scNP and S2P-scNP vaccines as a three-dose regimen or as a heterologous boost for S2P mRNA-LNP vaccine.
(A) Negative-stain electron microscopy 2D class averaging of RBD-scNP, NTD-scNP, and S2P-scNP. The size of each box: RBD-scNP and NTD-scNP, 257 Å; S2P-scNP, 1,029 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-AF + Alum. Monkeys were then challenged with SARS-CoV-2 WA-1, collected for blood, BAL and nasal swab samples, and necropsied for pathologic analysis. (C) Neutralization ID50 of plasma antibodies (week 0, 2, 6 and 10) against pseudotyped SARS-CoV-2 D614G strain in 293T/ACE2.MF cells. (D) Neutralization ID50 of the NTD-scNP-induced antibodies (week 10) against live SARS-CoV-2 WA-1 virus in Vero-E6 cells in microneutralization (MN) assay. (E-F) Plasma antibody neutralization against pseudoviruses of the SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. (E) ID50 titers and (F) reduction of ID50 titers against variants were shown as fold reduction compared to the titers against WA-1. (G) NTD-scNP- or S2P-scNP-induced plasma antibody (post-2nd and post-3rd immunization) neutralization titers against pseudoviruses of the SARS-CoV-2 Omicron variants in 293T-ACE2 cells. The geometric mean ID50 titers and the fold reduction compared to D614G are shown. (H) SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. (I) Histopathological analysis. Scores of lung inflammation determined by H&E staining and SARS-CoV-2 nucleocapsid antigen expression determined by IHC staining. (J) 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, collected for blood, BAL and nasal swab samples, and necropsied for pathologic analysis. (K-L) Plasma antibody neutralization against pseudoviruses of SARS-CoV-2 variants in 293T-ACE2-TMPRSS2 cells. (K) ID50 titers. (L) Reduction of ID50 titers against variants were shown as fold reduction compared to the titers against WA-1. (M) Plasma antibody (post-2nd and post-3rd immunization) neutralization titers against pseudoviruses of the SARS-CoV-2 Omicron variants in 293T-ACE2 cells. The geometric mean ID50 titers and the fold reduction compared to D614G are shown. The dashed arrow indicates fold increase of ID50 titer induced by the 3rd boost. (N) SARS-CoV-2 N gene sgRNA in BAL and nasal swab samples collected on day 2 and 4 post-challenge. (O) Histopathological analysis. Scores of lung inflammation determined by H&E staining and SARS-CoV-2 nucleocapsid antigen expression determined by IHC staining. ns, not significant, *P<0.05, Wilcoxon rank sum exact test.
See this image and copyright information in PMC

References

    1. Arvin A.M., Fink K., Schmid M.A., Cathcart A., Spreafico R., Havenar-Daughton C., Lanzavecchia A., Corti D., and Virgin H.W. (2020). A perspective on potential antibody-dependent enhancement of SARS-CoV-2. Nature 584, 353–363. 10.1038/s41586-020-2538-8. - DOI - PubMed
    1. Baden L.R., El Sahly H.M., Essink B., Kotloff K., Frey S., Novak R., Diemert D., Spector S.A., Rouphael N., Creech C.B., et al. (2021). Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N Engl J Med 384, 403–416. 10.1056/NEJMoa2035389. - DOI - PMC - PubMed
    1. Baiersdorfer M., Boros G., Muramatsu H., Mahiny A., Vlatkovic I., Sahin U., and Kariko K. (2019). A Facile Method for the Removal of dsRNA Contaminant from In Vitro-Transcribed mRNA. Mol Ther Nucleic Acids 15, 26–35. 10.1016/j.omtn.2019.02.018. - DOI - PMC - PubMed
    1. Benjamini Y., and Hochberg Y. (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological) 57, 289–300.
    1. Berry J.D., Jones S., Drebot M.A., Andonov A., Sabara M., Yuan X.Y., Weingartl H., Fernando L., Marszal P., Gren J., et al. (2004). Development and characterisation of neutralising monoclonal antibody to the SARS-coronavirus. J Virol Methods 120, 87–96. 10.1016/j.jviromet.2004.04.009. - DOI - PMC - PubMed

Publication types