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VanLaraklios

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Team develops 2 nasal sprays to prevent virus transmission
« on: August 07, 2024, 09:23:58 PM »

https://uh.edu/news-events/stories/2024/august/08062024-varadarajan-nanosting-rx-and-vaccine.php

[*quote*]
University of Houston

University of Houston Researchers Create New Treatment and Vaccine for Flu and Various Coronaviruses

Team Develops Two Nasal Sprays – An Immune Activator and a New Vaccine – To Prevent Virus Transmission

By Laurie Fickman — 713-743-8454
August 06, 2024 —

    Health and Medicine
    Research

A small vial labeled “NanoSTING” with a blue cap. The vial is on a laboratory surface.
NanoSTING (and NanoSTING-SN) developed at UH to fight COVID and flu

Researcher Ankita Leekha in a lab coat and safety goggles examines a small vial, standing in a laboratory setting.
Researcher Ankita Leekha with a bottle of NanoSTING

HOUSTON, Aug. 6 — A team of researchers, led by the University of Houston, has discovered two new ways of preventing and treating respiratory viruses. In back-to-back papers in Nature Communications, the team — from the lab of Navin Varadarajan, M.D. Anderson Professor of William A. Brookshire Chemical and Biomolecular Engineering - reports the development and validation of NanoSTING, a nasal spray, as a broad-spectrum immune activator for controlling infection against multiple respiratory viruses; and the development of NanoSTING-SN, a pan-coronavirus nasal vaccine, that can protect against infection and disease by all members of the coronavirus family. 

NanoSTING Therapeutic’s Highlights

    NanoSTING, a nasal spray, can prevent multiple respiratory viruses by activating the immune system and preventing infection from viruses. It can also protect against SARS-CoV-2 reinfection.
    A single intranasal dose of the NanoSTING has proven effective against strains of SARS-CoV-2 and the flu virus.
    NanoSTING is complementary to vaccines and enables cells to be in a heightened state of alert to prevent attack from respiratory viruses.

NanoSTING-NS Pan-coronavirus Vaccine’s Highlights

    UH researchers have developed NanoSTING-SN, a nasal vaccine that prevents transmission to the unvaccinated and fights multiple COVID variants.
    NanoSTING-SN provides the exciting potential towards a universal coronavirus vaccine and may end the cycle of onward transmission and viral evolution in immunocompromised people.
    Intramuscular vaccines prevent disease but are less efficient in preventing infections. NanoSTING-SN can provide improved protection against transmission for COVID variants and related sarbecoviruses. 

NanoSTING

NanoSTING is a special formula that uses tiny fat droplets to deliver an immune-boosting ingredient called cGAMP. This formula helps the body's cells stay on high alert to prevent attack from respiratory viruses. 

“Using multiple models, the team demonstrated that a single treatment with NanoSTING not only protects against pathogenic strains of SARS-CoV-2 but also prevents transmission of highly transmissible variants like the Omicron variants,” reports Varadarajan. “Delivery of NanoSTING to the nose ensures that the immune system is activated in the nasal compartment and this in turn prevents infection from viruses.”
Navin Varadarajan smiling at the camera in a laboratory setting, wearing a striped shirt.
Navin Varadarajan, M.D. Anderson Professor of William A. Brookshire Chemical and Biomolecular Engineering, is fighting the flu and coronavirus - professionally - in his lab!

As the recent COVID19 pandemic illustrated, the development of off-the-shelf treatments that counteract respiratory viruses is a largely unsolved problem with a huge impact on human lives.

“Our results showed that intranasal delivery of NanoSTING, is capable of eliciting beneficial type I and type III interferon responses that are associated with immune protection and antiviral benefit,” reports first author and postdoctoral associate, Ankita Leekha.

The authors further show that NanoSTING can protect against both Tamiflu sensitive and resistant strains of influenza, underscoring its potential as a broad-spectrum therapeutic.

“The ability to activate the innate immune system presents an attractive route to armoring humans against multiple respiratory viruses, viral variants and also minimizing transmission to vulnerable people,” said Leekha. “The advantage of NanoSTING is that only one dose is required unlike the antivirals like Tamiflu that require 10 doses.”

The mechanism of action of NanoSTING is complementary to vaccines, monoclonal antibodies and antivirals, the authors noted.
Nano STING-SN

Despite the successful implementation of multiple vaccines against SARS-CoV-2, these vaccines need constant updates due to viral evolution, plus the current generation of vaccines only offers limited protection against transmission of SARS-CoV-2.

Enter NanoSTING-SN, a multi-antigen, intranasal vaccine, that eliminates virus replication in both the lungs and the nostrils and has the ability to protect against multiple coronaviruses and variants.

“Using multiple preclinical models, the team demonstrated that the vaccine candidate protects the primary host from disease when challenged with highly pathogenic variants. Significantly, the vaccine also prevents transmission of highly transmissible variants like the Omicron variants to vaccine-naïve hosts,” reports Varadarajan.

The authors further show that the nasal vaccine was 100% effective at preventing transmission of the Omicron VOCs to unvaccinated hosts.

“The ability to protect against multiple coronaviruses and variants provides the exciting potential towards a universal coronavirus vaccine,” said Leekha. “The ability to prevent infections and transmission might finally end this cycle of onward transmission and viral evolution in immunocompromised people.”

The research was conducted by a collaborative team at UH including Xinli Liu, College of Pharmacy and Vallabh E. Das, College of Optometry along with Brett L. Hurst of Utah State University and consultation from AuraVax Therapeutics, a spinoff from Varadarajan’s Single Cell Lab at UH, which is developing NanoSTING.

Funding for the studies was provided by NIH (R01GM143243), Owens Foundation, and AuraVax Therapeutics.

    Health and Medicine
    Research

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VanLaraklios

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Re: Team develops 2 nasal sprays to prevent virus transmission
« Reply #1 on: August 07, 2024, 09:28:20 PM »

https://www.nature.com/articles/s41467-024-50234-y

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Nature Communications

An intranasal nanoparticle STING agonist protects against respiratory viruses in animal models
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    Article
    Open access
    Published: 18 July 2024

An intranasal nanoparticle STING agonist protects against respiratory viruses in animal models

    Ankita Leekha, Arash Saeedi, Monish Kumar, K. M. Samiur Rahman Sefat, Melisa Martinez-Paniagua, Hui Meng, Mohsen Fathi, Rohan Kulkarni, Kate Reichel, Sujit Biswas, Daphne Tsitoura, Xinli Liu, Laurence J. N. Cooper, Courtney M. Sands, Vallabh E. Das, Manu Sebastian, Brett L. Hurst & Navin Varadarajan

Nature Communications volume 15, Article number: 6053 (2024) Cite this article

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Abstract

Respiratory viral infections cause morbidity and mortality worldwide. Despite the success of vaccines, vaccination efficacy is weakened by the rapid emergence of viral variants with immunoevasive properties. The development of an off-the-shelf, effective, and safe therapy against respiratory viral infections is thus desirable. Here, we develop NanoSTING, a nanoparticle formulation of the endogenous STING agonist, 2′−3′ cGAMP, to function as an immune activator and demonstrate its safety in mice and rats. A single intranasal dose of NanoSTING protects against pathogenic strains of SARS-CoV-2 (alpha and delta VOC) in hamsters. In transmission experiments, NanoSTING reduces the transmission of SARS-CoV-2 Omicron VOC to naïve hamsters. NanoSTING also protects against oseltamivir-sensitive and oseltamivir-resistant strains of influenza in mice. Mechanistically, NanoSTING upregulates locoregional interferon-dependent and interferon-independent pathways in mice, hamsters, as well as non-human primates. Our results thus implicate NanoSTING as a broad-spectrum immune activator for controlling respiratory virus infection.
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Introduction

Within the last 20 years, we experienced four global respiratory epidemics/pandemics: severe acute respiratory syndrome (SARS) in 2003, influenza H1N1 in 2009, Middle East respiratory syndrome coronavirus in 2012, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019. These pandemics added to the global burden of existing threats like seasonal Influenza and respiratory syncytial virus (RSV)1,2. The recent COVID-19 pandemic caused by SARS-CoV-2 has led to 6.17 million deaths (April 2022), while current outbreaks driven by new variants of concern (VOCs) continue to be reported worldwide. Three classes of interventions comprise the modern arsenal of responses against respiratory viruses: vaccines, antibodies, and antivirals3,4,5. All these three interventions require significant time for identification and characterization of the virus, development, and rapid testing to identify the emerging pathogen, followed by manufacturing and global distribution of therapeutics or vaccines. With regards to rapidly mutating viruses such as RNA viruses, all these three modalities are prone to failure due to the high mutation rate of the virus coupled with insufficient and ineffective protection, which facilitates the evolution of resistant variants6,7,8.

Respiratory viruses enter the body and initiate replication in the respiratory tract. In response to the initial infection, the host elicits a multi-faceted innate immune response, typically characterized by the antiviral interferon (IFN) response, and the ensuing battle between the host immune system and the virus dictates the progression and outcome of infection9,10. Despite the IFN antagonistic mechanisms evolved by pathogens, these innate immunity responses dominate in most individuals and result in primarily asymptomatic infection or localized illness in the airways, still permitting an onward transmission of the virus11,12. If the host’s innate immune response is suboptimal for any reason, including genetic defects or autoantibodies against IFNs, the viral infection progresses, leading to disseminated disease and even mortality13,14. Ensuring robust antiviral innate immune responses in the airways is central to controlling viral infection, replication, transmission, and disease outcomes. Although conceptually straightforward, harnessing this host antiviral response is challenging. Direct administration of IFN proteins in clinical trials for COVID-19 has yielded mixed results with undesirable side effects15,16. It is thus clear that the location, duration, and timing of host-directed immunotherapies are necessary to ensure the activation of the appropriate antiviral pathways that balance efficacy without causing tissue damage and toxicity.

The stimulator of the interferon genes (STING) pathway is an evolutionarily-conserved cellular sensor of cytosolic double-stranded DNA (dsDNA), enabling a broad innate immune response against viruses17,18. Mechanistically, activation of STING fosters an antiviral response that involves not just the type I and III interferons (IFN-I and IFN-III) but also additional pathways independent of interferon signaling19,20. In humans, pre-activated STING-mediated immunity in the upper airways controls early SARS-CoV-2 infection in children and can explain why children are much less susceptible to advanced disease21,22. Multiple reports have demonstrated that supra-physiologic activation of STING inhibits replication of viruses, including coronaviruses, and that viruses have evolved mechanisms to prevent the optimal activation of STING within the host22,23.

Here, we demonstrate that intranasal delivery of a nanoparticle formulation of cyclic guanosine monophosphate–adenosine monophosphate (cGAMP), termed NanoSTING, enables the sustained release of cGAMP to both the nasal compartment and the lung for upto 48 h. We tested the ability of NanoSTING to protect against multiple VOCs of SARS-CoV-2 in hamsters and various variants of influenza A in mice. In these animal models, NanoSTING treatment prevented clinical disease, improved survival, reduced viral titers by several orders of magnitude, reduced transmission, and enabled durable protection from reinfection. In non-human primates, single- and repeat-dose administration of NanoSTING activated innate immunity in the nasal compartment. The stability, ease of administration, and the comprehensive nature of the immune response elicited make NanoSTING a promising, broad-spectrum antiviral, independent of the type of respiratory virus and variants.
Results
Preparation, characterization, and stability of NanoSTING

NanoSTING is a negatively charged liposomal formulation encapsulating endogenous STING agonist, cGAMP, optimized for the delivery of cGAMP to the respiratory tract (Fig. 1A).24,25,26 The composition of the lipids in our liposomal formulation has been shown to promote delivery to alveolar macrophages, facilitating the initiation of innate immune responses in the upper airways and the lung27,28. Dynamic light scattering (DLS) analysis revealed that the mean particle diameter of NanoSTING was 100 nm, with a polydispersity index of 23.6% (Supplementary Fig. 1A). The zeta potential of NanoSTING was −47 mV (Supplementary Fig. 1B). We confirmed the ability of NanoSTING to induce interferon responses by using THP-1 monocytic cells modified to conditionally secrete luciferase downstream of an Interferon regulatory factor (IRF) responsive promoter (Supplementary Fig. 1C). We stimulated THP-1 dual cells with NanoSTING at doses ranging from 2.5 to 10 µg and performed kinetic measurements for 24 h by measuring the luciferase activity in the supernatant. We observed a low level of luciferase activity at 6 h, and secretion was maximal at 24 h with 5 µg and 10 µg NanoSTING (Supplementary Fig. 1D). To evaluate the impact of NanoSTING on cell viability, we measured the change in the percentage of dead cells after treatment using dynamic live cell imaging. Tracking the difference in the percentage of dead cells after 12 h of treatment with 2.5–10 µg of either cGAMP or NanoSTING revealed that stimulation by NanoSTING did not impact cell viability (Supplementary Fig. 1E). We next systematically measured the stability of the nanoparticles by assessing particle sizes and zeta potential of NanoSTING at two different temperatures, 25 °C, and 37 °C. While the hydrodynamic diameter of NanoSTING was essentially unchanged at 25 °C over a period of 30 days (Supplementary Fig. 1F), there was a slight increase in hydrodynamic diameter at 37 °C after 2 weeks (mean: 114 nm at 25 °C and 154 nm at 37 °C) [Supplementary Fig. 1G]. We did not observe a change in zeta potential at either temperature (−45 mV at 25 °C and 37 °C) [Supplementary Table 1]. These results demonstrate that NanoSTING remains stable even without refrigeration.
Fig. 1: Pharmacokinetic and pharmacodynamic profiling of NanoSTING reveals prolonged delivery of cGAMP and induction of ISGs in the nasal compartment of mice.
figure 1

A Overall schematic for the synthesis of NanoSTING and intranasal delivery of NanoSTING to mice. Groups of 3–12 BALB/c mice were treated with single doses of NanoSTING (10 µg, 20 µg, or 40 µg) and we euthanized subsets at 6 h, 12 h, 24 h, 36 h, and 48 h followed by collection of blood, nasal turbinates, and lungs. cGAMP ELISA, IFN-β ELISA, CXCL10 ELISA, and qRT-PCR (nasal turbinates) were the primary readouts. B, C ELISA quantification of cGAMP in the nasal turbinates and lungs of mice after treatment with NanoSTING. D–L Fold change in gene expression for NanoSTING-treated (40 µg in green, 20 µg in red, and 10 µg in blue) mice and control mice were quantified using RNA extracted from nasal turbinates by qRT-PCR (Primer sequences are provided in Supplementary Table 2). M Quantification of IFN-β concentration in mouse nasal tissue using quantitative ELISA. N, O Quantification of CXCL10 levels in mouse nasal tissue and lungs using quantitative ELISA. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse. P-values were calculated by a two-tailed Mann–Whitney U-test for (B–O) ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Data presented as combined results from (B–O) one independent animal experiment. Gender was not tested as a variable, and only female mice were included in the study. See also Supplementary Figs. 1–3 and Supplementary Table 2. Color codes: 40 µg NanoSTING (green), 20 µg NanoSTING (red), 10 µg NanoSTING (blue) and Control (black). A Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 3–12/group. Source data are provided as a Source Data file.
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NanoSTING delivers cGAMP across mucosa, leading to sustained Interferon-beta (IFN-β) secretion in the nasal compartment

Although cGAMP is a potent natural activator of STING, its clinical utility is hampered by a lack of cellular penetration and rapid degradation by plasma ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), leading to an in vivo half-life of only ∼35 min29. We first characterized the ability of NanoSTING to mediate the delivery of cGAMP in the nasal compartment of mice. We delivered varying amounts of NanoSTING (10–40 μg) intranasally to groups of BALB/c mice, harvested the nasal turbinates and lungs, and assayed cGAMP using quantitative ELISA (Fig. 1A). We observed a dose-dependent increase in the concentration of cGAMP in the nasal turbinates; at the low dose (10 μg), we quantified cGAMP upto 12 h with a return to baseline at 24 h, whereas at the higher doses (20–40 μg), we detected cGAMP for 24 h with a return to baseline at 48 h (Fig. 1B). In the lungs, cGAMP was only detectable at the higher concentrations (20 and 40 μg) [Fig. 1C]. We also profiled the sera of these animals and observed that cGAMP was not detected at any time points in circulation, even at the highest dose (40 μg) [Supplementary Fig. 2]. These data confirmed that NanoSTING can transport cGAMP to the cells of the nasal passage in a concentration and time-dependent manner without systemic exposure.

The biological implications of NanoSTING’s ability to deliver cGAMP and thus activate the STING pathway were evaluated using a panel of 10 genes to measure the immune response comprehensively. The panel comprised of the effector cytokines, C–X–C motif chemokine ligand 10 (Cxcl10) and interferon beta (Ifnb); Interferon stimulated genes (ISG) including Isg15, Interferon regulatory factor 7 (Irf7), myxovirus resistance proteins 1 and 2 (Mx1 and Mx2), and Interferon-induced protein with tetratricopeptide repeats 1 (Ifit1); and non-specific pro-inflammatory cytokines (Il6 and Tnf). BALB/c mice received varying doses of intranasal NanoSTING, and quantitative qRT-PCR was performed on the nasal turbinates (6–48 h) [Fig. 1A]. The effector cytokines Cxcl10 and Ifnb showed maximal induction (7000–20,000-fold) that remained elevated at 48 h (Fig.1D, E). The five ISGs demonstrated strong induction from 6 h (300–1000-fold) to 24 h, followed by a decline from 24 to 48 h (Fig. 1F–I and Supplementary Fig. 3). NanoSTING’s inflammatory response was linked to the IFN pathway as the pro-inflammatory cytokine Il6 showed brief induction at 6 h (5000-fold), declined significantly by 24 h, and returned to baseline levels at 48 h (Fig. 1J). Furthermore, Tnf and Il10 showed only weak induction (15–60-fold) [Fig. 1K, L]. To rule out non-specific inflammation as the reason for the Ifnb1 responses in nasal turbinates, we intranasally administered groups of mice with liposomes without encapsulated cGAMP (Supplementary Fig. 4A, B). The Ifnb1 responses in animals administered with liposomes without encapsulated cGAMP were 100-fold lower than those in animals administered with NanoSTING, confirming that cGAMP is required for the robust induction of Ifnb1 (Supplementary Fig. 4C). Collectively, these results demonstrate that NanoSTING elicits a rapid and sustained inflammatory response triggering both effector cytokines and ISGs, but only minimal activation of non-specific pro-inflammatory cytokines.

Since the qRT-PCR data suggested strong induction of the effector cytokines, Ifnb and Cxcl10, we quantified the concentration of IFN-β and CXCL10 proteins in the nasal turbinates. Consistent with the transcriptional data, quantitative ELISA confirmed that both IFN-β and CXCL10 could be detected in the nasal turbinates and lungs for up to 24 h (Fig. 1M–O). We also tested the sera of the same animals. We did not observe either IFN-β or CXCL10 (Supplementary Fig. 2), confirming that the stimulation of innate immunity by intranasal NanoSTING was localized in the airways without associated induction of systemic pro-inflammatory activity.
Cellular targets of NanoSTING-mediated activation

To track the cellular targets of NanoSTING, we synthesized liposomes by encapsulating sulphorhodamine (SRB), a red fluorescent dye with a charge and size similar to cGAMP. After synthesizing the liposomes, we conjugated them to DiD, a green fluorescent lipophilic carbocyanine dye. We dosed groups of mice intranasally with these dual-colored liposomes, harvested the lung and nasal turbinates at 12 h, and analyzed single-cell suspensions using flow cytometry (Fig. 2A). The frequency of the cells that were DiD+SRB+ was higher in the nasal tissue (6.4 ± 0.9%) compared to the lung (0.5 ± 0.2%) [Fig. 2B, C]. In both tissues, we specifically focused on four major subtypes of cells: epithelial cells (CD45−EPCAM+CD31−), endothelial cells (CD45−CD31+), and two myeloid cell subsets with the phenotype (i) CD45+EPCAM−CD11b+CD11c− and (ii) CD45+EPCAM−CD11c+CD11b− [Fig. 2D].
Fig. 2: Uptake of NanoSTING by myeloid populations and epithelial cells in nasal tissue and lungs.
figure 2

A Overall schematic for tracking the cellular targets of NanoSTING. The liposomes were formulated to encapsulate SRB (red dye) and the liposomes were conjugated to DiD (green dye). The dual-labeled liposomes were administered intranasally to mice, and the single-cell suspensions were analyzed using flow cytometry. The cell types of the murine nasal epithelium are shown schematically. B Quantification of DiD+ SRB+ cells in lungs and nasal tissue by flow cytometry. C Flow cytometric plots (pseudocolor-smooth) showing uptake of DiD & SRB in nasal tissue. D Quantification of DiD+ SRB+ epithelial cells (CD45−EPCAM+), endothelial (CD45−CD31+), and two myeloid cell subsets-CD45+EPCAM−CD11b+CD11c− and CD45+EPCAM−CD11c+CD11b− in lungs and nasal tissues by flow cytometry. E Flow cytometric plots (pseudocolor-smooth) showing uptake of DiD & SRB by epithelial cells in nasal tissue. F The percentages of epithelial cells (basal cells, secretory cells & ciliated cells) in nasal tissue. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse. Data presented as combined results from (B–F) one independent animal experiment. Gender was not tested as a variable, and only female mice were included in the study. See also Supplementary Fig. 5 (gating strategy), Supplementary Table 4 (list of antibodies or conjugates used). Color codes: Lungs (Black), Nasal tissue (gray). A Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 5/group. Source data are provided as a Source Data file.
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Comparing the nasal turbinates and lungs, the frequency of the epithelial cells that were DiD+SRB+ was higher for nasal turbinates (14.6 ± 3%) than for the lungs (0.1 ± 0%). We further investigated the three major subsets of epithelial cells in the nasal turbinates that were DiD+SRB+: secretory cells showed the highest frequency of DiD+SRB+ (41 ± 2%), followed by basal cells (33 ± 2%) and ciliated cells (26 ± 1%) [Fig. 2E, F]. In both tissues, only a low frequency of DiD+SRB+ cells were endothelial cells (Fig. 2D). Within the myeloid cell populations, we observed a higher frequency of CD45+EPCAM−CD11b+CD11c− cells in nasal tissue (76.2 ± 7%) compared to lung (41 ± 8%). Conversely, the frequency of CD45+EPCAM−CD11c+CD11b− was notably higher in the lung (43 ± 6%) compared to nasal tissue (4 ± 1%) [Fig. 2D, E]. In aggregate, the flow cytometry data revealed that NanoSTING is preferentially distributed to the nasal compartment, and activates the myeloid cell populations and diverse epithelial cell subsets within the nasal compartment.
Repeat-dose administration of NanoSTING is safe and well-tolerated in mice and rats

We first studied biodistribution by altering the transport volume of intranasally delivered NanoSTING. It has been previously demonstrated that lower volumes lead to more efficient delivery to the nasal passage while larger volumes facilitate delivery to the lung30. Intranasal administration of Evan’s blue dye in low and high volumes (40 μL and 120 μL) resulted in staining of the nasal turbinates, lungs, and stomach in hamsters (Supplementary Fig. 6A–C). However, at both volumes, there was a significant amount of the dye delivered to the nasal turbinates and lung (intended target organs) [Supplementary Fig. 6A], and the normalized ratio of distribution to these tissues was independent of the volume of administration (Supplementary Fig. 6B, C). These results suggested that biodistribution to the lung/nasal compartments after intranasal delivery of liquid formulations was not impacted by the volume of inoculum.

To investigate if the liposomal nanoparticle formulation can lead to toxicity, we administered a single dose of nanoparticles (without encapsulated cGAMP) to mice. We harvested the lungs and stomach (Supplementary Fig. 7A). Histopathology of all these organs was unremarkable, confirming that the lipid components, when formulated as nanoparticles, are not toxic (Supplementary Fig. 7B). To investigate the toxicology of NanoSTING, we used allometric scaling based on both the body mass and nasal surface (intranasal delivery) to identify the appropriate doses for intranasal delivery to rats. We administered a low dose of 50 μg (low dose, equivalent to 10 μg in mice) and 250 μg (high dose, equivalent to 40 μg in mice) intranasally to groups of rats, performed routine clinical observations, and monitored the weight daily. There was no significant difference in food consumption, body weight changes, loss of fur, or any other clinical observations between the treatment and control groups for either sex. Similarly, hematology, coagulation, clinical chemistry, and urinalysis were normal in the NanoSTING-treated rats (Supplementary Tables 5–8).

Repeat-dose toxicity studies are vital to drug development and help identify potential toxicity in the appropriate target organs. We administered groups of rats four doses of NanoSTING (125 μg, mid-dose). We harvested the small intestines, stomach, lungs, and nasal cavity (Fig. 3A). Histopathology of all these organs was unremarkable, confirming that repeat-dose administration of NanoSTING is safe (Fig. 3B). Similarly, hematology, coagulation, clinical chemistry, and urinalysis were all normal upon repeat-dose administration of NanoSTING (Supplementary Tables 9–12). In aggregate, these results demonstrated that repeat-dose administration of NanoSTING did not affect any toxicological parameters in animals.
Fig. 3: Rat toxicology studies based on repeat-dose administration of NanoSTING.
figure 3

A Groups of Sprague Dawley rats (n = 12) were intranasally administered four doses of 125 µg on the indicated days and euthanized on day 11 for histopathology of the small intestines, lungs, nasal cavity, and stomach. B Representative H & E images of the target organs of the treated rats; all images were acquired at 10×; scale bar, 100 µm. Gender was tested as a variable with an equal number of male and female rats included in the study. See Supplementary Figs. 6, 7. A Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 12/group. Source data are provided as a Source Data file.
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RNA-sequencing confirms a robust IFN-I signature in the lungs of hamsters following intranasal NanoSTING administration

Next, we wanted to investigate the impact of intranasal NanoSTING administration on the lungs of Syrian golden hamsters (Mesocricetus auratus). The hamster is a well-characterized model for the SARS-CoV-2 challenge and mimics severe disease in humans; animals demonstrate easily quantifiable clinical disease characterized by rapid weight loss, very high viral titers in the lungs, and extensive lung pathology31. Additionally, unlike the K18-hACE2 transgenic model, hamsters recover from the disease (like most humans) and hence offer the opportunity to study the impact of treatments in the disease process and virus transmission31,32.

To assess the impact of intranasal NanoSTING on the lung, we administered one group (n = 4/group) of hamsters with daily doses of NanoSTING (60 µg) for four consecutive days. We used naive hamsters as controls (n = 4/group). Both groups of hamsters showed no differences in clinical signs, such as temperature or body weight (Supplementary Fig. 8A, B). On day 5, we isolated the lungs from hamsters for unbiased whole-transcriptome profiling using RNA-sequencing (RNA-seq). At a false-discovery rate (FDR q-value < 0.25), we identified a total of 2922 differentially expressed genes (DEGs) between the two groups (Fig. 4A). A type I IFN response was induced in NanoSTING-treated lungs, comprising canonical ISGs, including Mx1, Isg15, Uba7, Ifit2, Ifit3, Ifit35, Irf7, Adar, and Oas2 (Fig. 4B)33. The effector cytokines, Cxcl9-11 and Ifnb, were also induced in treated hamsters (Fig. 4C) and showed robust induction of direct antiviral proteins, such as Ddx60 and Gadd45g (Fig. 4D)34,35. We performed gene set enrichment analysis (GSEA) to compare the differentially induced pathways upon treatment with NanoSTING. We interrogated the changes in these populations against the Molecular Signatures Database (Hallmark, C2, and C7 curated gene sets). We observed a distinct cluster of pathways related to both type I and type III interferons in the lungs of NanoSTING-treated mice. We confirmed the specificity of the response by qRT-PCR analyses by quantifying Mx1-2, Isg15, Irf7, Cxcl11, Ifnb, Il6, and Il10 (Supplementary Fig. 9). Since the gene signature of interferon-independent activities of STING is known19, we performed GSEA and confirmed that NanoSTING activates interferon-independent pathways (Fig. 4E, F). In aggregate, these results demonstrate that cGAMP-mediated activation of STING by NanoSTING efficiently engages both interferon-dependent and interferon-independent antiviral pathways in the lung.
Fig. 4: RNA-sequencing identifies the activation of IFN-dependent and IFN-independent pathways in the lungs of hamsters treated with NanoSTING.
figure 4

A Heatmap of the top 50 differentially expressed genes (DEGs) between NanoSTING-treated lungs (marked as green) and control lungs (marked as black). B The volcano plots of DEGs comparing NanoSTING-treated and control animals. C Gene set enrichment analyses (GSEA) of C2 and C7 curated pathways visualized using Cytoscape. Nodes (red and blue circles) represent pathways, and the edges (blue lines) represent overlapping genes among pathways. The size of nodes represents the number of genes enriched within the pathway, and the thickness of edges represents the number of overlapping genes. The color of nodes was adjusted to an FDR q-value ranging from 0 to 0.25. Clusters of pathways are labeled as groups with a similar theme. D The normalized enrichment score (NES) and false-discovery rate (FDR) q values of top antiviral pathways curated by GSEA analysis. E GSEA of IFN-independent activities of STING pathway activated in the lung of NanoSTING-treated animals. The schematic represents the comparison that was made between samples collected from the GSE149744 dataset to generate the pathway gene set. F The expression of genes in lungs associated with IFN-dependent and IFN-independent antiviral pathways between NanoSTING and control groups. Data represents independent biological replicates taken from separate animals. Data presented as combined results from one independent animal experiment. Gender was tested as a variable with an equal number of male and female hamsters included in the study. See also Supplementary Figs. 8 and 9 and Supplementary Table 3. Color codes: Control (Black), NanoSTING (green). Fig. 1A-Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 4/group.
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Quantitative modeling predicts that early treatment with NanoSTING will dampen viral replication

The in vivo mechanistic experiments demonstrated that NanoSTING induces a broad antiviral response by engaging the innate immune system. To investigate potential efficacy, we used a mathematical model in combination with human viral titer data to identify the treatment window and quantify the relative amount of type I IFN (or related pathways) elicited by NanoSTING required for therapeutic benefit36,37. To simplify the framework of the model, we assumed that in vivo cGAMP only works to stimulate interferon responses. With this assumption, we modeled the range of relative interferon ratios (RIR, 0–1) we need to elicit via NanoSTING in comparison to the population level peak interferon responses observed upon SARS-CoV-2 infection (Fig. 5A, B) (equation 1 and 2) [Refer to Sup Note 1] and investigated the influence on viral elimination. Based on the model, an RIR of just 0.27 (27% of natural infection) would be sufficient to achieve a 50% reduction in viral titer (based on the area under the curve, AUC), and RIR values of at least 0.67 would achieve a 100% reduction in viral titers (Fig. 5C). We next modeled the window of initiation of treatment, which revealed that intervention would be most effective when initiated within 2 days after infection (Fig. 5D). By contrast, if the treatment is initiated after the peak of viral replication, even with an RIR of 1, improvement in outcomes cannot be readily realized (Fig. 5D and Supplementary Fig. 10C). Collectively, these results from quantitative modeling predicted that: (i) a single dose of NanoSTING is adequate to elicit only a moderate amount of IFN which is likely achievable since our data supports large induction of IFN-β (Figs. 1E, M, and 4F) and given that natural infections with viruses like SARS-CoV-2 and Influenza A are known to suppress interferon production38,39,40, and (ii) the optimal treatment window was either as prophylaxis treatment or initiated early after infection.
Fig. 5: Quantitative modeling of the dynamics of replication of SARS-CoV-2.
figure 5

A, B Schematic representing rate constants and equations governing viral dynamics during A natural infection and B in the presence of NanoSTING treatment. C Reduction in the viral area under the curve (AUC) at different NanoSTING efficacies (RIR) compared to natural infection. The treatment is initiated on day 0, and we assume that the effects of NanoSTING treatment only last for 24 h. D Heatmap of viral AUC with varying NanoSTING efficacy and treatment initiation time. The red box represents the combination with close to 100% reduction in viral AUC. See Supplementary Fig. 10, Supplementary Tables 13–15, and Supplementary Note 1. Fig. 5A, B Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en).
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NanoSTING protects against the SARS-CoV-2 Delta VOC

Based on the prediction of the modeling studies, we evaluated whether a single dose of NanoSTING protects hamsters from SARS-CoV-2 infection. The SARS-COV2 Delta VOC (B.1.617.2) was chosen because it causes upper- and lower-respiratory tract diseases and has increased disease severity compared to prior VOCs (Wuhan and Beta strains).41 We treated groups of 12 Syrian golden hamsters with a single intranasal dose of 120 µg NanoSTING, and 24 h later, we infected the hamsters with ∼3 × 104 50% Cell culture infectious dose (CCID50) of the Delta VOC via intranasal route (Fig. 6A). In the placebo-treated (PBS) group, hamsters exhibited weight loss, with a mean peak weight loss of 8 ± 2%. By contrast, hamsters treated with NanoSTING were largely protected from weight loss (mean peak weight loss of 2.7 ± 0.7%) (Fig. 6B, C). This small amount of weight loss in hamsters was similar to the results obtained by adenoviral vectored vaccines challenged with either the Wuhan or Beta strains42. We quantified the infectious viral titers by sacrificing six hamsters on day 2. Even with the highly infectious Delta VOC, NanoSTING reduced infectious viral titers in the lung post-two days of infection by 300-fold compared to placebo-treated animals (Fig. 6D). This reduction in lung viral titers closely correlates with weight loss prevention in these animals and models protection similar to clinical human disease. We also quantified the viral titers in the nasal compartment. We observed that treatment with NanoSTING reduced infectious viral titers in the nasal compartment post-two days of infection by 1000-fold compared to placebo-treated animals (Fig. 6E). The reduction in viral replication in the nasal compartment models the propensity of human transmission and confirms that treatment with NanoSTING decreases the likelihood of transmission. To map the duration of efficacy of prophylactic NanoSTING treatment, we administered a single intranasal dose of NanoSTING (120 µg) and challenged the hamsters 72 h later with ∼3 × 104 CCID50 of the Delta VOC (Supplementary Fig. 11A). Even when administered 72 h before exposure, NanoSTING showed moderate protection from weight loss and a significant reduction in infectious viral titers (Supplementary Fig. 11B–D). Our model also predicts that NanoSTING can be used to control infection after viral exposure. To test efficacy post-exposure, we delivered intranasal NanoSTING 6 h after exposure to the Delta VOC (Supplementary Fig. 12A). We observed a 340-fold and 13-fold reduction in infectious virus in the nasal passage and lung, respectively (Supplementary Fig. 12B, C). These results showed that a single-dose treatment with NanoSTING can effectively minimize clinical symptoms, protect the lungs, and reduce infectious viruses in the nasal passage.
Fig. 6: Protective efficacy of NanoSTING against the pathogenic SARS-CoV-2 Delta (B.1.617.2) VOC and IFN evasive SARS-CoV-2 Alpha VOC (B.1.1.7).
figure 6

A We treated groups of 12 Syrian Golden hamsters, each with a single dose of 120 µg NanoSTING, and later challenged with ∼3 × 104 CCID50 of SARS-CoV-2 Delta VOC on day 0 by the intranasal route. We euthanized half of the hamsters (n = 6) hamsters on day 2 and determined viral titers of lung and nasal tissues. We rechallenged the remaining 6 hamsters on day 28 and tracked the body weight change until day 35. B Percent body weight change compared to the baseline at the indicated time intervals. C Percent body weight change monitored during the primary infection (day 0–day 6). D, E Viral titers measured by endpoint titration assay in nasal tissues and lungs post-day 2 of infection. The dotted line indicates the limit of detection of the assay (LOD). F Percent body weight change monitored after rechallenge (day 28–day 35). G We tested groups of 9 hamsters, each with two different doses of NanoSTING (30 µg and 120 µg) and 24 h later challenged with the ∼3 × 104 CCID50 of SARS-CoV-2 Alpha VOC (B.1.1.7). On day 2, five animals from each group were euthanized for assessing the viral titers and remaining animals used for the histopathology at day 5. No animals were excluded in this study. H Change in body weight of hamsters. I, J Pathology scores and a representative hematoxylin and eosin (H & E) image of the lung showing histopathological changes in lungs of hamsters treated with NanoSTING (30 µg) and PBS; all images were acquired at 10× and 20×; scale bar, 100 µm. K, L Viral titers were quantified in the lung and nasal tissue by endpoint titration assay on day 2 after the challenge. The dotted line indicates the limit of detection of the assay (LOD). Individual data points represent independent biological replicates taken from discrete samples; vertical bars show mean values with error bars representing SEM. Each dot represents an individual hamster. For (D, E, I, K, L), analysis was performed using a two-tailed Mann–Whitney U-test. For (C, H), data was compared via a mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. Asterisks indicate significance compared to the placebo-treated animals at each time point. Mann–Whitney U-test ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. For (B), the p-values are as follows: Day 4: p = 6e−3, Day 5: p = 1e−3, and Day 6: p = 5e−5. For (H), the exact p-values comparing the 30 µg NanoSTING group to the Placebo group are Day 3: p = 5e−3, Day 4: p = 6e−7, and Day 5: p = 10e−9. Additionally, for the 120 µg NanoSTING and Placebo-treated group, the p-values are Day 4: p = 2e−5 and Day 5: p = 3.5e−9. Data presented as combined results from two independent experiments [A−F Challenge study with SARS-CoV-2 Delta VOC, G−L challenge study with SARS-CoV-2 Alpha VOC)], each involving one independent animal experiment. Gender was tested as a variable, and an equal number of male and female hamsters were included in the study. See also Supplementary Figs. 11 and 12. Figure 6A, G—Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used in the study: n = 12/group (for A−F), n = 9/group (for G–L). Source data are provided as a Source Data file.
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Treatment with NanoSTING induces protection against SARS-CoV-2 reinfection

One of the advantages of enhancing innate immunity to clear a viral infection is that this process mimics the natural host defense and minimizes the danger of clinical symptoms. We hypothesized that NanoSTING treatment via innate immune system activation also facilitates immunological memory against reinfection without additional treatment. To test this hypothesis, we intranasally treated Syrian golden hamsters (n = 12/group) with NanoSTING (120 µg) and 24 h later challenged with ∼3 × 104 of the SARS-CoV-2 Delta VOC (B.1.617.2) (Fig. 6A). On day 28, we rechallenged the hamsters with the Delta VOC. The untreated animals suffered significant weight loss during the primary challenge but were largely protected during the secondary challenge (Fig. 6F). By contrast, NanoSTING-treated hamsters showed minimal weight loss during the primary challenge, which did not compromise immunological memory. Indeed, NanoSTING-treated hamsters were completely protected from weight loss during the secondary challenge, and their body weight was identical to animals that were not previously challenged (Fig. 6F). These results suggest that a single intranasal treatment with NanoSTING activates the antiviral program of innate immunity, preventing clinical disease during primary infection while offering durable protection from reinfection.
NanoSTING treatment protects against the SARS-CoV-2 Alpha VOC

We next evaluated the impact of treatment with varying doses of NanoSTING and varied the dose of treatment based on the duration of response that we have documented (Fig. 1). The SARS-COV2 Alpha VOC (B.1.1.7) is known to be resistant to IFN-1 signaling in vitro and thus provides a challenging model to test the efficacy of NanoSTING43,44. We pre-treated Syrian golden hamsters (n = 6/group) with two intranasal doses of NanoSTING (30 μg and 120 μg) and 24 h later challenged the hamsters with ∼3 × 104 CCID50 of the Alpha VOC (Fig. 6G). Treatment with either dose of NanoSTING protected the hamsters from severe weight loss (Fig. 6H). We used an integrated scoring rubric (range from 1 to 12) that accounts for the histopathology of the lung tissue on day six after the viral challenge. We observed that NanoSTING-treated hamsters had significant reductions in aggregate pathology scores with minimal evidence of invasion by inflammatory cells or alveolar damage (Fig. 6I, J). In addition, we quantified the viral titers in the lungs and nasal compartments. We observed a significant reduction of viral titers in both compartments as early as day two post-challenge (Fig. 6K, L). Thus, treatment with intranasal NanoSTING reduces in vivo replication of SARS-CoV-2 by orders of magnitude and confers protection against IFN-I evasive strains of SARS-CoV-2.
NanoSTING treatment prevents infection in hamsters exposed to the SARS-CoV-2 Omicron VOCs

The SARS-CoV-2 Omicron VOC (BA.5) is among the most infectious strains of SARS-CoV-2. Using the Omicron VOC sets a high bar for NanoSTING to prevent viral transmission. We set up a transmission experiment designed to answer two fundamental questions: (1) does the prophylactic treatment of infected (index) hamsters prevent transmission to contact hamsters, and (2) does the post-exposure treatment of contact hamsters mitigate viral replication? Accordingly, we set up an experiment with three groups (n = 15) of Syrian golden hamsters. In each group, five index hamsters were intranasally infected with the ∼3 × 104 CCID50 of the SARS-CoV-2 Omicron VOC (BA.5). We quantified the viral titers in the infected and contact hamsters that were: (a) cohoused with placebo-treated infected index hamsters (group 1), (b) cohoused with NanoSTING (120 µg) treated index hamsters (group 2), or (c) treated with NanoSTING after cohousing with infected but untreated hamsters (group 3) [Fig. 7A]. The animals were co-housed continuously for 4 days such that transmission could happen through aerosols and also direct contact and fomite (including diet and bedding).
Fig. 7: Intranasal administration of NanoSTING limits transmission and viral replication in the lungs and nasal passage of contact hamsters exposed to the SARS-CoV-2 Omicron (BA.5) VOC.
figure 7

A Experimental setup: For group 1, we challenged groups of 5 hamsters each on day 0 with ∼3 × 104 of SARS-CoV-2 Omicron VOC (BA.5) and after 24 h cohoused index hamsters in pairs with contact hamsters (n = 5) for 4 days in clean cages. In group 2, we pre-treated the hamsters with 120 µg of NanoSTING 24 h prior to infection. In group 3, we treated the contact hamsters with NanoSTING 12 h after the cohousing period began. We euthanized the contact and index hamsters on day 4 of cohousing. Viral titers in the nasal tissue of the index and contact hamsters were used as primary endpoints. B Viral titers were quantified in the lung of the index (infected) and contact hamsters by endpoint titration assay post-day 5 of infection. C Viral titers were quantified in the nasal tissue of index and contact hamsters by endpoint titration assay post-day 5 of infection. The dotted line indicates the limit of detection of the assay (LOD). For (B, C) analysis was performed using a two-tailed Mann–Whitney U-test. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual hamster. Asterisks indicate significance compared to the placebo-treated animals. ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Data presented as combined results from one (B, C) independent animal experiment. NT Non-treated, NS-Pro Prophylactic treatment with NanoSTING, NS-Tx Post-exposure treatment with NanoSTING. Gender was tested as a variable with an equal number of male and female hamsters included in the study. A and parts of B, C—Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 5/group. Source data are provided as a Source Data file.
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As with the other strains of SARS-CoV-2 that we tested, NanoSTING pre-treatment of the infected hamsters led to a 1000-fold and 160-fold decrease in the viral load in the lungs and nasal compartment on day five compared to untreated animals (Fig. 7B, C). The reduction in viral loads was accompanied by efficient prevention of transmission to cohoused but untreated hamsters (4/5 of animals were virus-free in the NanoSTING group compared to 0/5 virus-free in the untreated group) [Fig. 7B, C]. Significantly, post-exposure treatment of the contact hamsters was also effective at reducing viral titers, although the magnitude of reduction was smaller compared to the animals that were directly challenged with the virus (Fig. 7C).

We repeated these transmission studies with the SARS-CoV-2 Omicron VOC (B.1.1.529) (Fig. 8A). We observed that NanoSTING pre-treatment of the infected hamsters almost completely blocked transmission (7/8 animals treated were virus-free vs 1/8 untreated animals were virus-free) [Fig. 8B]. Significantly, post-exposure treatment of the contact hamsters was also effective at preventing infection (6/8 animals treated were virus-free), and all animals demonstrated a significant reduction in viral titers (Fig. 8C). Consistent with the known milder disease of the Omicron VOC, none of the infected animals showed weight loss (Supplementary Fig. 13)45. Collectively, these results directly demonstrate that NanoSTING treatment is highly effective at blocking transmission even with the highly infectious Omicron VOC.
Fig. 8: Intranasal administration of NanoSTING limits transmission and viral replication in the nasal passage of contact hamsters exposed to the SARS-CoV-2 Omicron (B.1.1.529) VOC.
figure 8

A Experimental setup: For group 1, we challenged groups of 8 hamsters each on day 0 with ∼3 × 104 of SARS-CoV-2 Omicron VOC (B.1.1.529) and after 24 h cohoused index hamsters in pairs with contact hamsters (n = 8) for 4 days in clean cages. In group 2, we pre-treated the hamsters with 120 µg of NanoSTING 24 h prior to infection. In group 3, we treated the contact hamsters with NanoSTING 12 h after the cohousing period began. We euthanized the contact and index hamsters on day 4 of cohousing. Viral titers in the nasal tissue of the index and contact hamsters were used as primary endpoints. B, C Infectious viral particles in the nasal tissue of contact hamsters at day 2 and day 5 after viral administration post-infection were measured by endpoint titration assay. The dotted line indicates limit of detection of the assay (LOD). For (B, C), analysis was performed using a two-tailed Mann–Whitney U-test. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual hamster. Mann–Whitney test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Data presented as combined results from one (B, C) independent animal experiment. Gender was tested as a variable with an equal number of male and female hamsters included in the study. See supplementary Fig. 13. Abbreviations- NS-Pro: Prophylactic treatment with NanoSTING; NS-Tx-Post-exposure treatment with NanoSTING. A and parts of B, C—Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en) Number of animals: n = 8/group. Source data are provided as a Source Data file.
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Treatment with NanoSTING induces protection from influenza superior to oseltamivir

Influenza viruses have evolved multiple mechanisms to dampen the host’s innate immunity, including the attenuation of interferon responses by the NS1 protein46,47. One of the primary treatment options against influenza involves post-exposure treatment using oseltamivir, which inhibits the influenza neuraminidase protein. We thus compared the efficacy of NanoSTING in comparison to oseltamivir in mouse models of influenza.

We challenged groups of ten mice with 2 × 104 CCID50 of Influenza A/California/04/2009 (H1N1dpm). We treated them with a clinically relevant dose of oseltamivir (30 mg/kg/day) twice daily for five days (Supplementary Fig. 14A)48. The untreated animals started losing significant weight by day three and showed a mean peak weight loss of 31 ± 2.0%. By contrast, animals treated with oseltamivir were moderately protected, showing a mean peak weight loss of 21 ± 2.0% (Supplementary Fig. 14B). We next compared prophylaxis with either oseltamivir (two doses of 30 mg/kg/day) or NanoSTING (single dose at 40 µg) followed by challenge with 2 × 104 CCID50 of H1N1dpm (Fig. 9A). Prophylactic administration of oseltamivir was ineffective, as animals in the placebo (mean peak weight loss of 28 ± 1.0%) and oseltamivir-treated (mean peak weight loss 33 ± 3.0%) groups showed marked weight loss (Fig. 9B). By comparison, a single dose of NanoSTING offered strong longitudinal protection from weight loss (mean peak weight loss 15 ± 3%). These results demonstrate that prophylactic treatment with NanoSTING is superior to oseltamivir treatment.
Fig. 9: NanoSTING offers protection against Oseltamivir-sensitive and resistant strains of Influenza A.
figure 9

A Experimental set up: We treated groups of 10 BALB/c mice, each with a single dose of NanoSTING (40 µg) or Oseltamivir (30 mg/kg/day administered twice daily) or placebo and 24 h later challenged with 2 × 104 CCID50 of Influenza A/California/04/2009 (H1N1dpm) strain and monitored for 14 days. Body weight change was used as the primary endpoint. Oseltamivir was used as a control. B Percent body weight change for the different groups of mice. C Experimental set up: We treated groups of 10 BALB/c mice with a single intranasal dose of NanoSTING (40 µg) and 24 h later challenged with 2 × 104 CCID50 of influenza A/Hong Kong/2369/2009 (H1N1)-H275Y [A-H275Y] followed by rechallenge on day 28 and tracked the body weight change until day 35. We evaluated the animals for 41 days and used weight loss as the primary endpoint. On day 15, we evaluated the percent survival of different groups of mice. We conducted IgG and IgA ELISA on day 28. We treated one group of mice with a clinically relevant dose of oseltamivir, twice daily for five days. D Percent weight change compared to the weight at day 0 at the indicated time intervals. E Percent body weight change monitored after rechallenge (day 28–day 41). F Percent body weight change monitored during the primary infection (day 0–day 15). G Percent survival of the different groups of mice. H Humoral immune responses in the serum were evaluated on day 28 using IgG ELISA. I Humoral immune responses in the serum were evaluated on day 28 using IgA ELISA. J Experimental set up: We treated groups of 10 BALB/c mice with a single intranasal dose of NanoSTING (40 µg), and 24 h later challenged with 2 × 104 CCID50 of influenza A/Hong Kong/2369/2009 (H1N1)-H275Y [A-H275Y]. We monitored the animals for 7 days for body weight change and quantified viral titers at the end of the study. We treated one group of mice with oseltamivir, twice daily, for five days. K Weight change of the different groups of mice. L Viral titers were measured by endpoint titration assay in lungs post 7 days after infection. The dotted line indicates the limit of detection of the assay (LOD). For (H, I, L), analysis was performed using a two-tailed Mann–Whitney U-test. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse. For (B, F, K), weight data was compared via a mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. For (B, K), asterisks indicate statistically significant differences between the NanoSTING-treated group and placebo-treated animals, whereas, the pound sign shows statistically significant differences between the Oseltamivir-treated group and placebo-treated animals. For (F), asterisks indicate statistically significant differences between the NanoSTING-treated group and non-challenged animals, whereas, pound sign indicate statistically significant differences between the Oseltamivir-treated group and non-challenged animals. For (G) we compared survival percentages between NanoSTING-treated and Oseltamivir-treated animals using the Log-Rank Test (Mantel–Cox). ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. For (B) the exact p-values comparing the 40 µg NanoSTING group to the Placebo group are as follows: Day 2: p = 5e−3, Day 3: p = 5.5e−4, Day 4: p = 3e−4, Day 5: p = 2e−5, Day 6: p = 3e−7, Day: 8: p = 1e−4, Day 9: p = 4e−3, Day 10: p = 2.5e−2, Day 11: p = 1e−2, Day 12: p = 6e−3, Day 13: p = 6e−3, Day 14: p = 8e−3 and Day 15: p = 2e−2. Additionally, for the Oseltamivir and Placebo-treated group, the p-values are as follows: Day 2: p = 1e−2. For (F) the exact p-values comparing the 40 µg NanoSTING group to the Placebo group are as follows: Day 9: p = 5e−3. Additionally, for the Oseltamivir and Placebo-treated group, the p-values are as follows: Day 3: p = 6e−6, Day 4: p = 2e−8, Day 5: p = 10e−10, Day 6: p = 2e−10, Day 9: p = 6e−8, Day 10: p = 1e−3, Day 11: p = 1e−2. For (K) the exact p-values comparing the 40 µg NanoSTING group to the Placebo group are as follows: Day 3: p = 4e−2, Day 4: p = 5e−3, Day 5: p = 9e−4, Day 6: p = 7e−6, Day 7: p = 1e−5. The data combines results from three independent animal studies: Study 1 (A, B), Study 2 (C–I), and Study 3 (J–L), each involving one independent experiment. Gender was tested as a variable with an equal number of male and female mice included in the study. See also Supplementary Fig. 14. A, J—Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en) Number of animals used: n = 10/group. Source data are provided as a Source Data file.
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The evolution of resistance to treatment is predictable and common with influenza. A single amino acid mutation (His275Tyr) with neuraminidase has led to oseltamivir-resistant influenza viruses in humans49. Since NanoSTING relies on the host’s innate immune response and should be effective against treatment-resistant strains, we next evaluated its potency against oseltamivir-resistant influenza A in mice. We treated groups of ten mice with a single intranasal dose of NanoSTING (40 µg) and 24 h later challenged with 2 × 104 CCID50 of influenza A/Hong Kong/2369/2009 (H1N1)-H275Y [A-H275Y] (Fig. 9C). On day 28, we rechallenged the animals and monitored weight loss until day 41. We used changes in body weight and percent survival as primary endpoints, while serum IgG and IgA were used as secondary measures of adaptive immunity. We treated one group of mice with oseltamivir (30 mg/kg/day), twice daily for five days as a control48. NanoSTING-treated animals were well-protected from weight loss (mean peak weight loss of 8 ± 4.0%) in comparison to oseltamivir treatment (mean peak weight loss of 32 ± 3.0%) [Fig. 9D, F]. The weight loss in the NanoSTING-treated animals was transient between days 6–10, and outside of this window, the weight loss in the animals was no different from that of unchallenged animals (Fig. 9D, F). By contrast, starting at day 4, oseltamivir-treated animals showed significant weight loss until the end of the study (day 15). Consistent with these observations, 100% of NanoSTING-treated animals survived, whereas only 20% of oseltamivir-treated animals survived (Fig. 9G). HA-specific ELISA on day 28 (before rechallenge) confirmed robust IgA and IgG responses (Fig. 9H, I), demonstrating that NanoSTING protected from weight loss without compromising adaptive immunity and immunological memory. We confirmed that these immune responses are protective; upon rechallenge, the NanoSTING-treated animals were protected from weight loss (mean peak weight loss of 1.9 ± 0.2%) compared to non-challenged animals (mean peak of 3.4 ± 0.4%) [Fig. 9E]. Collectively, these results demonstrate that a single-dose treatment with NanoSTING protects against multiple strains of influenza by establishing immunological memory.

To test the impact of NanoSTING treatment on viral titers within the lung, we repeated the challenge experiments with influenza A-H275Y and euthanized the animals on day 7 (Fig. 9J). A single-dose treatment with NanoSTING again protected animals from weight loss (mean peak weight loss of 5 ± 2.0% vs. 32 ± 2.0% placebo) [Fig. 9K]. Infectious viral particles in the lung 7 days after viral exposure were reduced by 500-fold compared to the placebo-treated group, accounting for the ability of NanoSTING to help prevent disease and death (Fig. 9L). In aggregate, these experiments confirmed that NanoSTING works as a broad-spectrum antiviral against influenza by protecting from weight loss, reducing viral titers, and preventing death.
NanoSTING activates innate immunity in upper airways in Rhesus macaques

To assess the impact of NanoSTING on Rhesus macaques (M. mulatta), we administered intranasally four animals with two doses of NanoSTING (0.1 mg/kg-range: 0.06–0.14 mg/kg) on day 0 and day 2. We monitored the animals for four days to track changes in body weight, attitude, appetite, body temperature, and temperature of the nasal cavity (Fig. 10A). Based on our mice studies, we prioritized the measurement of CXCL10 to quantify the activation of innate immunity by NanoSTING. Accordingly, we performed a simple saline wash to collect the nasal fluid for assessments of CXCL10. None of the animals showed clinical signs such as loss of body weight (Fig. 10B) or an increase in body temperature (Fig. 10C) upon administration of NanoSTING. We recorded the temperature for the entire nasal area (Fig. 10D) and right/left nasal areas (Supplementary Fig. 15A, B) before and after NanoSTING administration with a typical facial thermogram. We saw no significant increase in nasal temperatures upon delivery of NanoSTING. ELISA measurements confirmed that we saw a significant increase in the concentration of CXCL10 in the nasal washes at 24 h after administration, and this was reset to baseline at 48 h (Fig. 10E). Repeat-dose administration of NanoSTING increased the concentration of CXLC10, similar to the effect mediated by the first dose (Fig. 10E). We euthanized one of these treated animals and collected the trachea and lungs. These tissues were processed for routine Hematoxylin and Eosin staining. Histopathological evaluation of the lungs and trachea was unremarkable, providing direct evidence that NanoSTING can safely activate innate immunity (Fig. 10F, G, and Supplementary Fig. 16).
Fig. 10: NanoSTING activates innate immunity in upper airways in Rhesus macaques.
figure 10

A Experimental set up: We administered one group (n = 4/group) of Rhesus macaques (RM’s) with two doses of NanoSTING (0.1 mg/kg-range: 0.06–0.14 mg/kg) administered intranasally on day 0 and day 2, and we monitored the animals until day 4 for changes in body weight, body temperature, and nasal area temperature. We euthanized one of the animals on day 4 to assess the histopathological changes in the lungs and trachea. B Percent body weight change for the RM’s at indicated time intervals. C Body temperature change for RM’s at indicated time intervals. D Monitoring of nasal area temperature pre and post-nasal wash collection/NanoSTING treatment. E Quantification of CXCL10 levels in the nasal wash of animals using quantitative ELISA. F, G Representative hematoxylin and eosin (H & E) images of the lungs and trachea of RM’s treated with two doses of NanoSTING (0.1 mg/kg-range: 0.06–0.14 mg/kg); all images were acquired at 2×; scale bar, 100 µm. For (B, C, D), the analysis was performed using Kruskal–Wallis test. For (E), we performed Mann–Whitney U-test. Individual data points represent independent biological replicates taken from separate animals. Kruskal–Wallis test, Mann–Whitney U-test ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Data presented as combined results from one (B–G) independent animal experiment. 3 female and 1 male RM’s were taken for the study. See also Supplementary Figs. 15 and 16. A-Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals: n = 4/group Source data are provided as a Source Data file.
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Discussion

The availability of prophylactic and post-exposure treatments that can prevent disease and reduce transmission of viruses is an urgent and unmet clinical need. Here, we have demonstrated that a single dose of intranasal NanoSTING can work as prophylactic and therapeutic against multiple respiratory viruses (and standard treatment-resistant variants).

The current pandemic has once again highlighted that our therapeutic arsenal against RNA viruses is inadequate. Vaccines are our preferred means of protection against SARS-CoV-2, but they suffer from three drawbacks. First, while the current generation of vaccines was tested at remarkable speed, even this rate of development lags as vaccines need to be custom-manufactured for each emerging virus. Second, the mutational plasticity of RNA viruses like SARS-CoV-2 facilitates their evolution, and newer variants with immune escape potential have emerged. This necessitates ongoing booster shots in adults to achieve at least transitory, complete protection from disease, even as the entire human population is not yet fully vaccinated against SARS-CoV-250,51. As the human experience with influenza has illustrated, requiring additional booster shots reduces human compliance, facilitating the spread of disease. Compounding this problem is that immunosuppressed vaccine recipients fail to be sufficiently protected, and reservoirs are emerging for SARS-CoV-2 outside of humans52. Third, despite the efficacy of the current intramuscular vaccines in preventing disease, they do not prevent transmission53. The evolution of the SARS-CoV-2 Omicron (B.1.1.529) VOC shows that viruses can quickly adapt to facilitate rapid spread using the nasal cavity as a sanctuary. Thus, while vaccines are necessary, they are not sufficient to fight RNA viruses.

Monoclonal antibodies targeting viruses, like vaccines, offer protection against respiratory disease but suffer from the same disadvantages as vaccines listed above. Furthermore, their window of use is limited as the emergence of SARS-CoV-2 VOCs such as Omicron can quickly render them ineffective50. Additionally, monoclonal antibodies are expensive and administered in a clinical setting, limiting their widespread use. NanoSTING offers an alternative by generating an immune response that appears advantageous for instilling immunity. Focusing on efficacy, intravenous prophylactic administration of antibody (12 h before challenge) in hamsters led to protection from surrogates of clinical disease (∼2–5% weight loss and ∼300-fold reduction in viral titers in the lung) albeit with no impact on transmission54,55. NanoSTING provides a broader window of administration (24–72 h), with comparable efficacy in reducing clinical disease surrogates while reducing transmission.

Oral antivirals that directly inhibit one or more viral proteins have been developed against SARS-CoV-2 (e.g., paxlovid and molnupiravir) and Influenza (Oseltamivir) are approved for use in humans but are also susceptible to viral evolution and resistance8. Furthermore, these therapeutics are designed as an oral post-exposure treatment to prevent clinical disease and have no impact on viral transmission56. In contrast to these pathogen-specific drugs, NanoSTING works broadly against multiple respiratory viruses, including oseltamivir-resistant influenza, highlighting its translational potential. Although we have not undertaken a direct comparative study, based on a review of the literature, the efficacy of NanoSTING compares favorably to the results with paxlovid and molnupiravir in small animal models. The fact that these antivirals are efficacious in humans (30–89% in reducing clinical disease with SARS-CoV-2) suggests that NanoSTING has promising clinical potential57.

Immunomodulators, including defective viral genome particles, cytokines, and small-molecule agonists, have been tested as antivirals. Defective interfering particles (DIPs) have incomplete genomes and, when administered therapeutically, inhibit replication of the wild-type virus58. Although these particles have demonstrated efficacy for SARS-CoV-2 and Influenza in mitigating disease in small animal models, the DIPs must be generated for each virus individually58,59. Defective viral genomes (DVGs) based on the poliovirus induce a broad IFN-I response and are protective against multiple viruses60. However, DVGs need to replicate in vivo after administration, and this limited replication is essential for their efficacy. However, their broad applicability is limited by concerns about both safety and the presence of pre-existing antibodies in vaccinated people. Lipid nanoparticles complexed with the defective genomes can mitigate these concerns and have shown efficacy against SARS-CoV-2 VOCs in K18-hACE2 mice; the generalizability of this approach in the absence of viral replication to other viruses has not been demonstrated60.

Direct administration of aerosolized interferons to engage antiviral innate immunity has been tested in animals and humans. In hamsters challenged with SARS-CoV-2, prophylactic or early administration of universal IFN reduces lung damage, provides moderate protection against weight loss (10% vs. 20% for untreated animals), and reduces infectious viral particles (100-fold)61,62. NanoSTING appears to offer superior efficacy when compared to these data. In humans, post-exposure treatment with nebulized IFN-α2b was associated with reduced in-hospital mortality compared to no administration of IFN-α2b. By contrast, administration of IFN-α2b more than five days after admission delayed recovery and increased mortality, suggesting that the timing of IFN-α2b administration is critical for efficacy63. The limited impact of IFN-α for COVID-19 mirrors its negligible efficacy as a prophylactic against Influenza in humans64. In comparison to nebulized interferons, intranasal administration of NanoSTING yields sustained but localized activation of interferons. In combination with the repeat-dose safety data and the in vitro stability data, intranasal NanoSTING thus provides a promising translational path.

Other synthetic small-molecule agonists of pattern recognition receptors (PRRs), including stem-loop RNA 14 (SLR14), a minimal RIG-I (Retinoic acid-inducible gene I) agonist, and STING agonist, diAbzl, have been tested against SARS-CoV-2 in K18-hACE2 mice22,44,65,66. A pair of recent studies specifically highlight the efficacy of diABZI-4 in inducing protective innate immune responses against SARS-CoV-2 in murine models, further emphasizing the potential of STING-mediated defenses against viral infections65,66. As with all small-molecule drugs, the safety, off-target activity, and pharmacokinetics of synthetic STING agonists must be thoroughly evaluated before translation. NanoSTING is comprised of naturally occurring lipids that have already been tested in humans and cGAMP, the immunotransmitter of danger signals that are conserved across mammals, including humans67. As illustrated, NanoSTING leads to safe and sustained delivery and consequently functions as a broad-spectrum antiviral.

Our data illustrate that NanoSTING is a promising immune activator, is safe, stable, and effective against multiple viruses and variants, and can activate innate immunity in non-human primates. It achieves its antiviral effects by rapidly engaging and sustaining activation of the STING pathway. Indeed, an advantage of using the natural immunotransmitter, cGAMP is that STING activation can lead to both IFN-dependent and independent activities to control viral replication19,20,67. NanoSTING exhibits a broad spectrum of activity against existing viruses; activating the innate response protects against current viruses and likely emerging threats. Furthermore, in animal models, NanoSTING minimizes clinical symptoms during primary infection while preserving durable protection from reinfection by eliciting immunological memory. This offers the potential to protect the host from secondary challenges without the need for retreatment. We envision intranasal NanoSTING as a treatment to prevent respiratory viral disease in vulnerable populations or to intervene in respiratory infections before etiology is determined rapidly.
Methods
Preparation of NanoSTING

The liposomes contained DPPC, DPPG, Cholesterol (Chol), and DPPE-PEG2000 (Avanti Polar lipids) in a molar ratio of 10:1:1:1. To prepare the liposomes, we mixed the lipids in CH3OH and CHCl3, and we evaporated them at 45 °C using a vacuum rotary evaporator. The resulting lipid thin film was dried in a hood to remove residual organic solvent. We hydrated the lipid film by adding a pre-warmed cGAMP (MedChemExpress) solution (3 mg/mL in PBS buffer at pH 7.4). We mixed the hydrated lipids at an elevated temperature of 65 °C for an additional 30 min and then subjected them to freeze-thaw cycles. Next, we sonicated the mixture for 60 min using a Branson Sonicator (40 kHz) and used Amicon Ultrafiltration units (MW cut off 10 kDa) to remove the free untrapped cGAMP. Finally, we washed the NanoSTING (liposomally encapsulated STINGa) three times using PBS buffer. We measured the cGAMP concentration in the filtrates against a calibration curve of cGAMP at 260 nm using the Take3 Micro-Volume absorbance analyzer of Cytation 5 (Bio-Tek). We calculated the final concentration of cGAMP in NanoSTING and encapsulation efficiency by subtracting the concentration of free drug in the filtrate.

To check the stability, we stored the NanoSTING at 24 °C and 37 °C for 1, 2, 3, 7, 14, and 30 days. We measured the average hydrodynamic diameter and zeta potential of liposomal particles using DLS and a zeta sizer on Litesizer 500 (Anton Paar).
Cell lines

THP-1 dual cell line (human, Invivogen: Cat No. thpd-nfis) was cultured in a humidified incubator at 37 °C and 5% CO2 and grown in RPMI/10% FBS (Corning, NY, USA). In addition, we supplemented the THP-1 dual cell line with the respective selection agents (100 μg/mL zeocin + 10 μg/mL blasticidin) and the corresponding selection cytostatics from Invivogen.
Cell stimulation experiments with luciferase reporter enzyme detection

We performed the cell stimulation experiments using the manufacturer’s instructions (Invivogen, CA, USA). First, we seeded the cells in a 96-well plate at 1 × 105 cells/well in 180 μL growth medium. Next, we made serial dilutions of NanoSTING on a separate plate at concentrations ranging from 2.5 to 10 µg/mL in the growth medium. We then incubated the cells at 37 °C for 24 h. To detect IRF activity, we collected 10 μL of culture supernatant/well at 6 h, 12 h, and 24 h and transferred it to a white (opaque) 96-well plate. Next, we read the plate on Cytation 7 (Cytation 7, Bio-Tek Instruments, Inc.) after adding 50 μL QUANTI-Luc™ (Invivogen) substrate solution per well, followed by immediate luminescence measurement. The data was recorded as relative light units (RLU).
Viability assessment of cGAMP and NanoSTING

THP-1 dual cells were resuspended in complete RPMI 1640 media supplemented with 10% FBS and 100 nM SYTOX green (Invitrogen, cat. # S34860). They were incubated on a 96-well plate at a density of 1,00,000 cells per well at 37 °C and 5% CO2. The cells were then stimulated with 2.5–10.0 µg of either cGAMP or NanoSTING. Wells containing unstimulated cells were used as control samples. The cells were imaged using a Cytation 7 inverted microscope using 20× Plan Fluorite WD 6.6 NA 0.45 objective from the FITC and Brightfield channels at 1 h and 12 h post-stimulation.

We detected and counted the number of dead cells and the total number of cells for each time point by segmenting objects from corresponding GFP and bright field images. For GFP images, we applied blob detection with Laplacian of Gaussian as kernel to detect the bright blobs and an overlapping threshold of 0.5. We picked the detections with a 1.2–5 µm radius and a Gaussian sigma value higher than 0.1, each representing one dead cell. On the other hand, for bright field images, we used the CellPose68 model to segment the cells. Specifically, we used the weights pre-trained by the original paper and followed the default setting of the CellPose detection workflow, except for increasing the flow error threshold to 0.8. As a result, we obtained individual detections and the number of cells for both GFP and bright field images. We calculated the percentage of dead cells as the number of GPF-positive cells normalized to the total number of cells at each time point and plotted the change in the percentage of dead cells after 12 h of stimulation.
Mice and NanoSTING treatment

All studies using animal experiments were reviewed and approved by the University of Houston (UH) IACUC. We purchased the female 7–9-week-old BALB/c mice from Charles River Laboratories (Strain code: 028). The mice were maintained within a Specific Pathogen-Free (SPF) facility housed on ventilated racks within microisolation caging systems. Notably, the mice were not bred within the facility premises and were cohoused during the study. The housing facility for mice was under a 12:12-h light: dark cycle at temperatures 20–22 °C, humidity 40–50%. After sedating them with isoflurane, we intranasally treated the groups of BALB/c mice (n = 3–12/group) with varying amounts of NanoSTING (10–40 μg). We euthanized the animals by cervical dislocation after 6 h, 12 h, 24 h, 36 h, and 48 h and harvested blood, nasal turbinates, and lungs. We kept the blood at room temperature (RT) for 10 min to facilitate clotting and centrifuged it for 5 min at 2000 × g. We collected the serum, stored it at −80 °C, and used it for ELISA.
ELISA

We homogenized nasal turbinates and lung tissue samples in 1:20 (w/v) of tissue protein extraction reagent (Thermo Fisher, # 78510), then centrifuged them for 10 min at 2500 × g to pellet tissue debris. Using quantitative ELISA, we assayed the supernatants for cGAMP, IFN-β, and CXCL10. cGAMP ELISA was performed using a 2′3′-cGAMP ELISA kit (Cayman Chemicals, MI, USA). IFN-β concentrations were tested using a mouse IFN-beta Quantikine ELISA kit (R&D Systems, MN, USA). Mouse IP-10 ELISA kit (CXCL10) was used to perform the CXCL10 ELISAs (Abcam, MA, USA). cGAMP, IFN-β, and CXCL10 concentrations were tested by titering 30 µg total protein from nasal turbinates and lung lysates. All serum samples were tested at 50× dilutions to test cGAMP, IFN-β, and CXCL10 concentrations.
RNA isolation, cDNA preparation, and qRT-PCR

We excised mouse nasal turbinate tissues and placed approximately 20 mg of tissue in 2 mL tubes containing 500 μL RNeasy lysis buffer (RLT) and a single stainless-steel bead. Next, we homogenized the tissue using a tissue lyser (Qiagen, Hilden, Germany) before total RNA extraction using an RNeasy kit (Qiagen, #74104), following the manufacturer’s instructions. Extracted RNA was treated with DNase using a DNA-free DNA removal kit (Invitrogen, #AM1906). Next, 1 µg of total RNA was converted to cDNA using a High-Capacity cDNA reverse transcription kit (Invitrogen, #4368813). We diluted the resultant cDNA to 1:10 before analyzing quantitative real-time polymerase chain reaction (qRT-PCR). We performed qRT-PCR reaction using SsoFastTM EvaGreen® Supermix with Low ROX (Biorad, # 1725211) on AriaMx Real-time PCR System (Agilent Technologies, Santa Clara, CA). We normalized the results to GAPDH (glyceraldehyde-3-phosphate dehydrogenase). We determined the fold change using the 2-DDCt method, comparing treated mice to naive controls. See Supplementary Table 2 for the primer sequences used in this study.
Single and repeat-dose toxicology study in rats
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We intranasally treated two groups (n = 12) of Sprague Dawley rats (10–12 weeks; Charles River; Strain code: 001) with a single dose of either 50 µg or 250 µg of NanoSTING. At 24 h after administration, a necropsy was performed. Similarly, we intranasally treated a group of 12 rats with four doses of NanoSTING (Days 1, 4, 7, 10), and a control group (n = 6) was used as a control group. An equal number of male and female rats were used in this study. A panel of toxicokinetics (TK)/Pharmacodynamics (PD), clinical pathology, and histopathology was performed by Product Safety Labs (New Jersey, USA) [Supplementary Tables 5–12].
Syrian golden hamsters

All studies using animal experiments were reviewed and approved by UH IACUC. We purchased the 6–10 week-old male and female hamsters (Mesocricetus auratus) from Charles River Laboratories (Strain code: 049). The hamsters were not bred on-site. All hamsters were singly housed while at the facility.
Safety studies of NanoSTING on Syrian golden hamsters

We designed a pilot study to test whether repeated NanoSTING administration causes clinical symptoms (fever or weight loss). We administered a group (n = 4/group) of animals with daily doses of 60 µg of NanoSTING intranasally for four consecutive days. We used naive hamsters as controls (n = 4/group). The animals were monitored daily for body weight change and body temperature. We euthanized using CO2 euthanasia the animals 24 h after administering the last dose and harvested lungs.
Processing of the hamster’s lungs for qRT-PCR and mRNA sequencing

Each lung was cut into 100–300 mm2 pieces using a scalpel to isolate single-cell suspension from the lungs. We transferred the minced tissue to a tube containing 5 mL of digestion Buffer containing collagenase D (2 mg/mL, Roche #11088858001) and DNase (0.125 mg/mL, Sigma #DN25) in 5 mL of RPMI (Corning, NY, USA) for 1 h and 30 min at 37 °C in the water bath with vortexing after every 10 min. We disrupted the remaining intact tissue by passaging (6–8 times) through a 21-gauge needle. After 1 h and 30 min of incubation, we added 500 µL of iced-stopping buffer (1× PBS, 0.1 M EDTA) to each falcon tube to stop the reaction. We then removed tissue fragments and the majority of the dead cells with a 40 µm disposable cell strainer (Falcon, #352340), and we collected the cells after centrifugation. We lysed the red blood cells by resuspending the cell pellet in 3 mL of ACK lysing Buffer (Gibco, #A1049201) and incubated for 3 min at RT, followed by centrifugation. We discarded the supernatants and resuspended the cell pellets in 5 mL of complete RPMI medium (Corning, NY, USA). We enumerated lung cells by trypan blue exclusion.
qRT-PCR and mRNA sequencing for hamster’s lung cells

Total RNA was extracted from whole lung cells using an RNeasy kit (Qiagen, #74104), following the manufacturer’s instructions. Extracted RNA was treated with DNase using a DNA-free DNA removal kit (Invitrogen, #AM1906). 1 µg of total RNA was converted to cDNA using a High-capacity cDNA reverse transcription kit (Invitrogen, #4368813). We diluted the resultant cDNA to 1:10 for qRT-PCR. We performed qRT-PCR reaction using SsoFastTM EvaGreen® Supermix with Low ROX (Biorad, #1725211) on AriaMx Real-time PCR System (Agilent Technologies, Santa Clara, CA). We normalized the results to Actb (β-actin gene). We determined the fold change using the 2-DDCt method, comparing treated mice to naive controls. The primer sequences are provided in Supplementary Table 3. The preparation of the RNA library and mRNA sequencing was conducted by Novogene Co., LTD (Beijing, China). We paired and trimmed the fastq files using Trimmomatic (v 0.39) and aligned them to the Syrian golden hamster genome (MesAur 1.0, ensembl) using STAR (v 2.7.9a). We determined the differential gene expression using DESeq2 (v 1.28.1) package69. To perform gene set enrichment analysis, we used a pre-ranked gene list of differentially expressed genes in GSEA software (UC San Diego and Broad Institute). To generate the gene set for IFN-independent activities of STING, we collected genes with a 2-fold change increase in BMDM-STING S365A-DMXAA vs BMDM-STING S365A-DMSO samples from the GSE149744 dataset as described previously19.
Preparation of DiD-SRB-loaded liposomes

We used liposomes composed of a molar ratio of 10:1:1:1 of DPPC, DPPG, Cholesterol (Chol), and DPPE-PEG2000. We added DiD to the lipid mixture with a 0.5 µmol/mL concentration. To prepare the liposomes, we mixed the lipids (16.9 mg of DPPC, 1.8 mg of DPPG, 0.9 mg of cholesterol, and 6.4 mg of DPPE-PEG2000) in 0.85 mL of chloroform and 0.341 mL of methanol in a round bottom flask. We vortexed this mixture to dissolve the lipids in the solvent solution. We made a stock of DiD solution. We added 1 gram of DiD to 50 mL of methanol and vortexed thoroughly. Next, we added 0.025 mL of this stock to the lipid/solvent mixture, then evaporated the solvents in the lipid mixture using a rotary evaporator (for 1 h) to form a lipid film. Next, we hydrated the lipid film by adding a pre-warmed 1 ml of SRB solution (50 mg/mL in PBS). Immediately after adding the SRB solution, the hydrated film should be vigorously vortexed. We mixed the hydrated lipids in a water bath at an elevated temperature of 65 °C (or a temperature above the transition temperature of the lipids) for an additional 30 min with vigorous vortexing every 5 min. The mixture was subjected to 10 freeze-thaw cycles by cooling it to −80 °C and warming it to RT (∼25 °C). Next, we extruded the mixture with an Avanti extruder kit at 65 °C using a 0.2 µm pore filter. The mixture should be passed through the filter 10 times or more. We performed NTA at this step on the liposomes. The mode of measurement 5 recording sets on the NanoSight NS300 Malvern Panalytical instrument at 10,000× dilution in milli-Q water. We removed the free untrapped SRB through dialysis (100 kDa membrane) for 24–48 h at 4 °C with continuous stirring and exchanged the PBS dialysate two times with fresh PBS. We characterized the DiD-SRB liposomes with a THP-1 assay and endotoxin assay.
Intranasal dosing of DiD-SRB liposomes to mice

We dosed a group of five BALB/c mice intranasally with DiD-SRB liposomes and euthanized the animals by cervical dislocation post 12 h. We harvested lungs and nasal tissues from indicated mice and processed them into single-cell suspensions for analysis by flow cytometry.
Tissue processing post DiD-SRB liposomes administration to mice

To isolate lung cells, we perfused the lung vasculature with 5 ml of 1 mM EDTA in PBS without Ca2+, Mg2+ and injected it into the right cardiac ventricle. Nasal tissue and lung were cut into 100–300 mm2 pieces using a scalpel. We transferred the minced tissue to a tube containing 5 ml of digestion buffer containing collagenase D (2 mg/ml, Roche #11088858001) and DNase (0.125 mg/ml, Sigma #DN25) in 5 ml of RPMI-1650 for 1 h and 30 min at 37 °C in the water bath by vortexing after every 10 min. We disrupted the remaining intact tissue by passage (6–8 times) through a 21-gauge needle. Next, we added 500 µL of ice cold-stopping buffer (1× PBS, 0.1 M EDTA) to stop the reaction. We then removed tissue fragments and dead cells with a 40 µm disposable cell strainer (Falcon) and collected the cells after centrifugation at 400 × g. We then lysed the red blood cells (RBCs) by resuspending the cell pellet in 3 ml of ACK Lysing Buffer (Invitrogen) and incubated for 3 min at RT, followed by centrifugation for 10 min at 400 × g. Then, we discarded the supernatants and resuspended the cell pellets in 5 ml of complete RPMI medium (Corning, NY, USA). Using the trypan blue exclusion method, we counted the lung and nasal tissue cells.
Cell surface staining for flow cytometry

We collected the cells and stained them with Live/Dead Aqua (Thermo Fisher #L34965) in PBS, followed by Fc-receptor blockade with anti-CD16/CD32 (Thermo Fisher #14-0161-85), and then stained for 30 min on ice with the following flourescent labeled antibodies/conjugates in flow cytometry staining buffer (FACS): anti-CD45, anti-EPCAM, anti-CD31, anti-CD11b, anti-CD11c, anti-CD24 and GS-IB4 conjugate. We washed the cells twice with the FACS buffer and analyzed them on LSR-Fortessa flow cytometer (BD Bioscience) using FlowJo™ software version 10.8 (Tree Star Inc, Ashland, OR, USA). Cell populations and subsets in the mouse respiratory system were gated and analyzed as described27. Information on various antibodies and conjugates and the dilution used is provided in Supplementary Table 4. See Supplementary Fig. 5 for the gating strategy.
Viruses

Isolates of SARS-CoV-2 were obtained from BEI Resources (Manassas, VA) and amplified in Vero E6 cells to create working stocks of the virus. Influenza A/California/04/2009 was kindly provided by Elena Govorkova (St. Jude Children’s Research Hospital, Memphis, TN) and was adapted to mice by Natalia Ilyushina and colleagues at the same institution. Influenza A/Hong Kong/2369/2009 (H1N1pdm) was provided by Kwok-Yung Yuen from The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China. The virus was adapted to mice by four serial passages in the lungs of mice, and plaque was purified at USU.
Biosafety

Studies with influenza virus were completed within the ABSL-2 space of the Laboratory Animal Research Center (LARC) at USU. Studies involving SARS-CoV-2 were completed within the ABSL-3 space of the LARC at USU.
Transmission studies

For group 1, we challenged groups of five hamsters each on day 0 with ∼3 × 104 of SARS-CoV-2 Omicron VOC (BA.5) and after 24 h cohoused index hamsters in pairs with contact hamsters (n = 5) for four days in clean cages. In group 2, we pre-treated the hamsters with 120 µg of NanoSTING 24 h prior to infection. In group 3, we treated the contact hamsters with NanoSTING 12 h after the cohousing period began. We repeated this study with another strain of Omicron VOC (B.1.1.529). Viral titers in the nasal tissue of the index and contact hamsters were used as primary endpoints. Infectious viral particles in the nasal tissue of contact hamsters on day 2 and day 5 after viral administration post-infection were measured by endpoint titration assay.
Viral challenge studies in animals

Animals. For SARS-COV-2 animal studies completed at USU, 6–10 week-old male and female golden Syrian hamsters (Strain code: 049) were purchased from Charles River Laboratories and housed in the ABSL-3 animal space within the LARC. For influenza virus animal studies, 8-week-old BALB/c (Strain code: 028) mice were purchased from Charles River Laboratories.

Infection of animals. Hamsters were anesthetized with isoflurane and infected by intranasal instillation of 1 × 104.5 CCID50 of SARS-CoV-2 in a 100 µl volume. Mice were also anesthetized with isoflurane and infected with a 1 × 104.3 CCID50 dose of influenza virus in a 90 µl volume.

Titration of tissue samples. Lung and nasal tissue samples from hamsters and lung tissue samples from mice were homogenized using a bead-mill homogenizer using minimum essential media. Homogenized tissue samples were serially diluted in a test medium and the virus was quantified using an endpoint dilution assay on Vero E6 cells [African green monkey kidney cells-Vero E6 (ATCC®, cat# CRL-1586′M)] for SARS-CoV-2 and on MDCK [Madin-Darby canine kidney- MDCK cells (ATCC®, CCL-34)] cells for influenza virus. A 50% cell culture infectious dose was determined using the Reed-Muench equation70.
Safety study in Rhesus macaques (RM’s)

Experiments with rhesus macaques (M. mulatta) were reviewed and approved by UH IACUC. Four healthy rhesus macaques (RM’s) of Indian origin, between 4 and 11 years of age and 4–12 kg in weight were used. The RM’s were acquired from Washington University School of Medicine, Division of Comparative Medicine C/O Dr. Chad B Faulkner; 660S. Euclid Ave., Box 8061; St. Louis, MO 63110 and Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX. We used four RM’s for the study. Three of them were males, and one was female. All the animals were single-housed. To assess the impact of NanoSTING on RM’s, we administered animals (n=4) with two doses of NanoSTING (700 µg) administered intranasally on day 0 and day 2. The animals were monitored until day 4 for changes in body weight, attitude, appetite, body temperature (via rectal thermometer), and nasal tract temperature using a Veterinary IR Pad 640, a digital thermal infrared camera (Digatherm Veterinary Thermal Imaging, Beaumont, TX). We collected the nasal wash each day for quantification of CXCL10 using quantitative ELISA. One animal was euthanized via intravascular (IV) injection of Euthasol euthanasia solution (Midwest Veterinary Supply). One of the RM’s was sedated using 55 mg Ketamine and 0.075 mg Dexmedetomidine (Midwest Veterinary Supply) IM (intramuscularly) before euthanasia on day 4 to assess any histopathological change in the lungs and trachea.
Histopathology

Lungs of the Syrian golden hamsters and lungs, trachea of Rhesus macaques and small intestines, stomach, lungs, and nasal cavity of rats were fixed in 10% neutral buffered formalin processed, paraffin-embedded, and 4-μm sections were stained with hematoxylin and eosin. We used an integrated scoring rubric for evaluating the pathology score71. The published scoring method was modified from a 0–3 to a 0–4 score with 1 = 1–25%; 2 = 26–50%; 3 = 51–75; and 4 = 76–100%. The original histologic criteria comprised of three compartments: airways, blood vessels, and interstitium. The sum of all three scores was reported as the cumulative lung injury score for an animal ranging from 0 to 12. This scoring also takes into account the degeneration/necrosis of the bronchial epithelium/alveolar epithelium. A board-certified pathologist (M.S.) evaluated the sections.
Quantitative modeling

To quantify the kinetics of SARS-CoV-2 infection in the upper respiratory tract (URT) in the presence of NanoSTING, we modified the innate immune model described by Ke et al.37. We added an additional coefficient to the term responsible for refractory responses in the set of governing ordinary differential equations (ODEs), as shown in supplementary information file (Supplementary Figs. 11 and 12). The mean population parameter values and initial values were taken from Ke et al.37. We solved the system of ODEs for different efficacies, treatment initiation time, and duration of response of NanoSTING using the ODE45 function in MATLAB 2018b. A sample MATLAB code for solving the system of equations has been provided in Supplementary Note 1.
Statistics and reproducibility

Statistical significance was assigned when P values were <0.05 using GraphPad Prism (v6.07). Tests, number of animals (n), mean values, statistical comparison groups, and the statistical test used are indicated in the figure legends. No statistical methods were used to predetermine sample sizes for the in vitro and animal studies. The sample size was determined based on similar studies in this field. Animal studies were randomized. When applicable, technical repeats are specified for each experiment in the figure legends wherever applicable. Reproducibility between animals in treatment and naïve controls/placebo-treated groups is shown in the results and figure legends. The researchers were not blinded to allocation during experiments and outcome assessment. Data collection and analysis were not performed blind to the conditions of the experiments. The pathologists performing the histopathological analysis were blinded to treatment. The formulation was manufactured at UH and shipped to USU. All animal experiments at USU were performed independently. Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Modeling SARS-CoV-2 infection

To quantify the kinetics of SARS-CoV-2 infection in the upper respiratory tract (URT) in the presence of NanoSTING, we used the innate immune model described by Ke et al.37. Assuming that NanoSTING efficacy is primarily due to the cell’s increased capacity to become refractory to infection, we modified the governing equations, as shown in the Supplementary Table 13 and Fig. 5 of the manuscript.

To get a physical interpretation of the variable NanoSTING, we non dimensionalized the target cell equation in the following way:
$$\frac{{{{{\rm{d}}}}}T}{{{{{\rm{d}}}}}t}=\,-{{{{\rm{\beta }}}}}{VT}-{{{{{\rm{\varphi }}}}}I}_{\max } \left(\frac{{{{{\rm{\varphi }}}}}I}{{{{{{\rm{\varphi }}}}}I}_{\max }}+\frac{{{{{\rm{NanoSTING}}}}}}{{{{{{\rm{\varphi }}}}}I}_{\max }}\right)T+{{{{\rm{\rho }}}}}R$$
(1)
$${{{{\rm{RIR}}}}}=\frac{{{{{\rm{NanoSTING}}}}}}{{{{{{\rm{\varphi }}}}}I}_{\max }}$$
(2)

Where RIR is the relative interferon ratio, which is the relative contribution of NanoSTING to antiviral Interferon (refractory) responses compared to peak antiviral Interferon responses during SARS-CoV-2 without NanoSTING.

We solved these ordinary differential equations with mean population parameter values and initial values taken from Ke et. al.37 and as shown in Supplementary Tables 14 and 15. First, we performed a sensitivity analysis to show that the peak natural SARS-CoV-2 response was independent of initial viral titer (Supplementary Fig. 10A). We also performed a sensitivity analysis to show that NanoSTING was effective at higher viral titers as well (Supplementary Fig. 10B). We calculated the viral titer area under the curve (AUC) during infection for varying RIRs and the treatment initiation time post viral exposure. Because the effect of NanoSTING lasts only for 24–48 h, the NanoSTING coefficient was non-zero only up to 24–48 h post-treatment initiation.
Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.
Data availability

All data are included in the Supplementary Information or available from the authors, as are unique reagents used in this Article. The raw numbers for charts and graphs are available in the Source Data file whenever possible. Sequencing data reported in this paper has been deposited to GEO (GSE201423) and is publicly available. All material and experimental data requests should be directed to the corresponding author, Navin Varadarajan. Source data are provided with this paper.
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Acknowledgements

This publication was supported by the NIH (R01GM143243), Owens Foundation, and AuraVax Therapeutics. We thank Prashant Menon and Kwan Ling Wu for helping with viability assessment studies.
Author information
Authors and Affiliations

    William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA

    Ankita Leekha, Arash Saeedi, Monish Kumar, K. M. Samiur Rahman Sefat, Melisa Martinez-Paniagua, Mohsen Fathi, Rohan Kulkarni, Kate Reichel & Navin Varadarajan

    College of Optometry, University of Houston, Houston, TX, USA

    Hui Meng & Vallabh E. Das

    Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA

    Sujit Biswas & Xinli Liu

    AuraVax Therapeutics, Houston, TX, USA

    Daphne Tsitoura, Laurence J. N. Cooper & Manu Sebastian

    Animal Care Operations, University of Houston, Houston, TX, USA

    Courtney M. Sands

    Institute for Antiviral Research, Utah State University, Logan, UT, USA

    Brett L. Hurst

Contributions

N.V. conceived the study. N.V., A.L., L.J.N.C., M.S., and B.H. designed the study. A.L., A.S., S.R.S., M.K., M.M.P., R.K., S.B., B.H., H.M., C.M.S., H.M., V.E.D. and X.L. performed experiments. A.L., A.S., S.R.S., M.K., K.R., B.H., X.L., D.T., and N.V. analyzed the data. M.K. performed modeling, and MF performed bioinformatic analyses. N.V. and A.L. drafted the manuscript and all authors contributed to the review and editing of the manuscript.
Corresponding author

Correspondence to Navin Varadarajan.
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Competing interests

UH has filed provisional patents based on the findings of this study. N.V. and L.J.N.C. are co-founders of AuraVax Therapeutics and CellChorus. The remaining authors declare no competing interests.
Ethics approval

The mouse, hamster, and NHP studies were performed under the study protocol (PROTO2020000019, PROTO202100006, PROTO202100049, PROTO202200025), as approved by the Institutional Animal Care and Use Committee in the University of Houston. The animal experiments at USU were conducted in accordance with an approved protocol by the Institutional Animal Care and Use Committee of Utah State University. The work was performed in the AAALAC-accredited LARC of the university in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals (8th edition; 2011).
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Leekha, A., Saeedi, A., Kumar, M. et al. An intranasal nanoparticle STING agonist protects against respiratory viruses in animal models. Nat Commun 15, 6053 (2024). https://doi.org/10.1038/s41467-024-50234-y

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    Received10 November 2022

    Accepted04 July 2024

    Published18 July 2024

    DOIhttps://doi.org/10.1038/s41467-024-50234-y

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    Published: 23 July 2024

Multi-antigen intranasal vaccine protects against challenge with sarbecoviruses and prevents transmission in hamsters

    Ankita Leekha, Arash Saeedi, K M Samiur Rahman Sefat, Monish Kumar, Melisa Martinez-Paniagua, Adrian Damian, Rohan Kulkarni, Kate Reichel, Ali Rezvan, Shalaleh Masoumi, Xinli Liu, Laurence J. N. Cooper, Manu Sebastian, Courtney M. Sands, Vallabh E. Das, Nimesh B. Patel, Brett Hurst & Navin Varadarajan

Nature Communications volume 15, Article number: 6193 (2024) Cite this article

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Abstract

Immunization programs against SARS-CoV-2 with commercial intramuscular vaccines prevent disease but are less efficient in preventing infections. Mucosal vaccines can provide improved protection against transmission, ideally for different variants of concern (VOCs) and related sarbecoviruses. Here, we report a multi-antigen, intranasal vaccine, NanoSTING-SN (NanoSTING-Spike-Nucleocapsid), eliminates virus replication in both the lungs and the nostrils upon challenge with the pathogenic SARS-CoV-2 Delta VOC. We further demonstrate that NanoSTING-SN prevents transmission of the SARS-CoV-2 Omicron VOC (BA.5) to vaccine-naïve hamsters. To evaluate protection against other sarbecoviruses, we immunized mice with NanoSTING-SN. We showed that immunization affords protection against SARS-CoV, leading to protection from weight loss and 100% survival in mice. In non-human primates, animals immunized with NanoSTING-SN show durable serum IgG responses (6 months) and nasal wash IgA responses cross-reactive to SARS-CoV-2 (XBB1.5), SARS-CoV and MERS-CoV antigens. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to reducing transmission of respiratory viruses, and (2) eliciting immunity against multiple antigens can be advantageous in engineering pan-sarbecovirus vaccines.
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Introduction

Humanity has undertaken one of the largest vaccination campaigns to protect all people against the respiratory virus SARS-CoV-2 and coronavirus-induced disease (COVID-19). mRNA (e.g., BNT162b2 and mRNA-1273) and adenovirus vector vaccines (e.g., ChAdOx1 nCoV-19) have been delivered intramuscularly (IM) to billions of recipients1,2. The evolution of variants of concern (VOC) like the Omicron VOCs has caused increase in infections even in countries with high vaccination coverage3. This increased frequency of infections combined with laboratory data that supports increased infectivity and immune escape by the variants has seeded concerns that we will end up in the cumbersome perpetual cycle of immunization trying to keep pace with evolving variants4,5,6,7.

There are two primary concerns with the commercial vaccines against SARS-CoV-2. First, while the IM route of administration elicits robust systemic immunity leading to the prevention of disease, they do not prevent viral infection in the upper airways. Unsurprisingly, the IM vaccines have demonstrated variable protection against upper-airway infection in preclinical models, with some offering no protection8,9. In humans, this led to both vaccinated and unvaccinated people harboring virus in the nostrils that facilitates transmission even by immunized individuals10,11. Moreover, the ability of the upper airways to serve as reservoirs facilitates viral evolution, and with the waning of vaccine-induced immunity over time, can enable the priming of new infections in vaccinated hosts12,13. The second concern is that the Spike (S) protein dominates the vaccine landscape against SARS-CoV-2 as the immunogen14. Since the S protein is essential for viral entry into host cells, it serves as the preferred target for eliciting neutralizing antibodies14,15. Although correlates of vaccine-induced protection have not been established, there is strong evidence that neutralizing antibodies, and specific antibodies targeting the receptor-binding domain (RBD) of the S protein, are likely predictors of vaccine efficacy and disease prevention16,17. The S protein, however, by being on the surface of the virion, is under constant evolutionary pressure to escape the host immune system while preserving viral entry18,19. Unsurprisingly, as the virus has spread globally, variants less susceptible to antibodies elicited by vaccines have evolved, necessitating modified vaccine manufacturing and continued booster immunizations19,20,21.

Among other potential viral protein targets, the nucleocapsid (N) protein is expressed at elevated levels during infection and is highly immunogenic22,23,24. Studies tracking convalescent patient sera confirm robust antibody and T-cell responses against the N protein25,26,27,28. The primary function of the N protein is to package the viral genome into ribonucleoprotein complexes and to facilitate transcription while promoting escape from innate immunity (suppression of type I interferons, IFNs)22. Since the N protein performs multiple essential functions for the virus, it tends to accumulate fewer mutations resulting in the N protein of SARS-CoV-2 having 90% homology to SARS-CoV29. These attributes make the N protein a candidate for vaccine-induced immunity23,24,30. Indeed, T-cell-dependent mechanisms can confer at least partial protection against the original Wuhan strain after IM vaccine candidates immunizing with the N protein31. However, preclinical studies have shown that transfer of the anti-N immune sera failed to protect against SARS-CoV-2 infection in an adapted mouse model32 which is consistent with antibodies against the N protein not being neutralizing as this protein is unassociated with viral entry. Furthermore, intradermal vaccination with the SARS-CoV N protein worsened infection and pneumonia due to T helper 2 (Th2) cell-biased responses33. This concern of enhanced respiratory disease mediated by Th2 responses has shifted the focus away from the SARS-CoV-2 N protein-based vaccines despite the potential for protective T-cell responses.

Mucosal vaccines can stimulate robust systemic and mucosal immunity, but the quality and quantity of the immune response elicited upon mucosal vaccination depend on the appropriate adjuvant. We had previously reported that liposomally encapsulated endogenous STING (stimulator of interferon genes) agonist (STINGa, 2’−3’ cGAMP), termed NanoSTING, functions as an excellent mucosal adjuvant that elicits strong humoral and cellular immune responses upon intranasal vaccination34. Here, we report that a multi-antigen intranasal subunit vaccine, NanoSTING-SN, delivers multi-factorial immunity by eliminating the virus from the nose and lung and prevents transmission to naïve animals. Our data provide a pathway to eliminating transmission of highly infectious variants and for engineering the next-generation vaccines that can protect against sarbecoviruses.
Results
Preparation and characterization of NanoSTING-S vaccine

NanoSTING is a liposomal adjuvant that comprises pulmonary surfactant-biomimetic nanoparticle formulated STINGa and enables mucosal immunity (Supplementary Fig. 1A)34,35. We synthesized NanoSTING, and dynamic light scattering (DLS) showed that the mean particle diameter of NanoSTING was 137 nm, with a polydispersity index (PDI) of 24.5% (Supplementary Fig. 1B) and a mean zeta potential of −63.5 mV (Supplementary Fig. 1C). We confirmed the ability of NanoSTING to induce IFN responses (IRF) using the THP-1 monocytic cells modified to conditionally secrete luciferase downstream of an IRF promoter. We stimulated THP-1 dual cells with NanoSTING and measured luciferase activity in the conditioned supernatant (Supplementary Fig. 1D) and showed that secretion was maximal at 24 h. We used recombinant trimeric S-protein to formulate the vaccine based on the SARS-CoV-2 B.1.351 (Beta VOC) as the immunogen36 (Fig. 1A). SDS-PAGE under reducing conditions showed that the protein migrated between 180 and 250 kDa, confirming extensive glycosylation (Supplementary Fig. 2A). Upon incubation with NanoSTING, the S protein was adsorbed onto the liposomes with NanoSTING-S (NanoSTING-Spike) displaying a mean particle diameter of 144 nm (PDI 25.9%), and a mean zeta potential of −54.8 mV (Supplementary Fig. 2B, C). Unlike the trimeric S protein known to aggregate in solution, we tested NanoSTING-S after 9 months of storage at 4 °C. We found no evidence of aggregation, concluding that the vaccine formulation is stable at 4 °C (Supplementary Fig. 2D, E).
Fig. 1: NanoSTING-S vaccine yields cross-reactive humoral and cellular immunity in mice and provides protective efficacy against Delta VOC in hamsters.
figure 1

A 3D structure of trimeric S protein (B.1.351) with the twelve mutations indicated (PDB: 7VX1)75. B Study timeline: We immunized BALB/c mice (n = 5/group) with a single dose of NanoSTING-S intranasally, followed by the collection of serum every week. We monitored the body weights of the animals every week after the immunization. We euthanized the animals by cervical dislocation at day 28 and then collected BALF, serum, lungs, and spleen. Primary endpoints were the body weight change, ELISA (IgG & IgA), and ELISPOT (IFNγ and IL4). Naïve BALB/c mice were used as controls (n = 4/group). C–F Humoral immune responses in the serum and BALF were evaluated using S-protein-based IgG & IgA ELISA. Splenocytes (G) or lung cells (H) were stimulated ex vivo with overlapping peptide pools, and IFNγ & IL4 responses were detected using an ELISPOT assay. I Experimental setup for challenge study in hamsters: We immunized Syrian golden hamsters (n = 10/group) intranasally with two doses of NanoSTING-S (first dose at day -42 and second dose at day -18, and challenged the hamsters intranasally with 3 × 104 CCID50 of the SARS-CoV-2 Delta VOC on day 0. Post challenge, we monitored the animals for 6 days for changes in their body weight. We euthanized half of the hamsters on day 2 and the other half at day 6 for histopathology of the lungs, with viral titers of lung and nasal tissues measured on day 2 and day 6. J Percent body weight change of hamsters compared to the baseline at the indicated time intervals. K, L Viral titers were measured by end-point titration assay in lungs and nasal tissues post-day 2 and day 6 of infection. The dotted line indicates the limit of detection of the assay (LOD). M, N Pathology score and a representative hematoxylin and eosin (H & E) image of the lung showing histopathological changes in hamsters treated with NanoSTING-S and PBS; all images were acquired at 10× & 20×; scale bar, 100 µm. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse/hamster. For (C–H, K, L, N), the analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns: not significant. For (J), the data was compared via mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. For (J), the exact p values comparing the NanoSTING-S group to the PBS group are Day 5: p = 5e-3, Day 6: p = 3.5e-4. Asterisks indicate significance compared to the PBS-treated animals at each time point. Data presented as combined results from two independent experiments [A–H: Immunogenicity study with NanoSTING-S, I–N: Challenge study with Delta VOC)], each involving one independent animal experiment. Gender was not tested as a variable, and only female mice were included in the study (A–H). Gender was tested as a variable with equal number of male and female hamsters included in study (I–N). See also Supplementary Figs. 1, 2, 3. B, I Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations - IN Intranasal. Number of animals used: A–H: n = 4–5/group, I–N: n = 10/group Source data are provided as a Source Data file.
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Single-dose immunization of mice with NanoSTING-S vaccine yields cross-reactive humoral and cellular immunity against SARS-CoV-2

We immunized BALB/c mice with a single intranasal dose of NanoSTING-S (Fig. 1B) and observed no clinical symptoms, including weight loss, during the entire 28-day period (Supplementary Fig. 3). We conducted ELISA on day 28 to quantify binding to both full-length S proteins and the RBDs, with the latter serving as a surrogate for neutralization37,38,39. We observed robust serum IgG titers not only against Beta (B.1.351) but also against Alpha (B.1.1.7), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) S proteins. We also observed high serum IgG titers against the RBDs from both the Beta and Alpha VOCs and high IgG titers against the full-length Beta and Delta spike proteins in bronchoalveolar lavage fluid (BALF, Fig. 1C, D). We evaluated the durability of the response upon vaccination at 5 months after immunization and confirmed high serum IgG titers (Supplementary Fig. 4). As IgA-mediated protection is an essential component of mucosal immunity for respiratory pathogens, we confirmed the role of intranasal NanoSTING-S as a mucosal vaccine candidate. We detected elevated serum IgA responses against all spike protein variants tested, although BALF IgA titers against full-length delta spike protein were weaker (Fig. 1E, F). At day 28, immunized mice showed robust and significant Th1/Tc1 responses by ELISPOT in both the spleen and the lung (Fig. 1G, H). We stimulated the spleen and lung cells with a pool of peptides containing mutations (B.1.351) in the S protein that differs from the Wuhan S protein. We observed a significant Th1 response against these mutation-specific S peptides, confirming a broad T-cell response that targets both the conserved regions and the mutated regions of the S protein (Fig. 1G, H). In contrast to the Th1/Tc1 responses, the Th2 responses were weaker but detectable (Fig. 1G, H). Collectively, these results established that NanoSTING acts as a mucosal adjuvant and that even a single-dose immunization with NanoSTING-S yielded robust IgG, IgA, and Th1/Tc1 responses that are cross-reactive against multiple VOCs.
NanoSTING-S elicited immune responses confer protection against the Delta VOC

The Syrian golden hamster (Mesocricetus auratus) challenge model was used to assess the protective efficacy of NanoSTING-S. This animal model replicates COVID-19 severe disease in humans with infected animals demonstrating rapid weight loss, very high viral loads in the lungs, extensive lung pathology, and even features of long COVID40,41. Additionally, unlike the K18-hACE2 transgenic mouse model, hamsters recover from the disease and hence offer the opportunity to study the impact of treatments in the lungs (disease) and nasal passage (transmission)40,42. We chose the SARS-CoV-2 Delta VOC to infect the animals for two reasons: (1) this VOC causes severe lung damage, and (2) Delta-specific S-mutations, including L452R and T478K within the RBD, are absent in our immunogen (Fig. 1A), providing an opportunity to assess cross-protection. We administered two doses of intranasal NanoSTING-S 24 days apart to hamsters, which were subsequently challenged with the Delta VOC through the intranasal route (Fig. 1I). Animals in the sham-vaccinated group showed a mean peak weight loss of 8 ± 2%. By contrast, animals vaccinated with NanoSTING-S were largely protected from weight loss (Fig. 1J), mean peak weight loss of 2.3 ± 0.7%, consistent with the results obtained by adenovirally vectored IM vaccines challenged with either the Wuhan or Beta strains43. We sacrificed half of the animals on day 2 (peak of viral replication) and the other half on day 6 (peak of weight loss in unimmunized animals) to quantify viral titers. NanoSTING-S reduced infectious viral loads in the lung by 300-fold by day 2 compared to sham-vaccinated animals, and by day 6, the infectious virus was undetectable in all animals (Fig. 1K). Viral replication in the lung of the animal models clinical human disease and death, while viral replication in the nasal compartment models human transmission. Immunization with NanoSTING-S reduced infectious viral loads in the nasal compartment by 380-fold by day 2 compared to unimmunized animals. By day 6, vaccinated animals showed a further significant reduction in the infectious virus (Fig. 1L). To examine the pathobiology of viral infection, we analyzed the lung tissue on day 6 after the challenge using an integrated scoring rubric (range from 1-12) to quantify host immune response and disease severity. We recorded immune cell infiltration and widespread viral pneumonia in the lungs of sham-vaccinated hamsters, whereas vaccinated animals revealed minimal evidence of invasion by inflammatory cells or alveolar damage (Fig. 1M, N). In aggregate, hamsters vaccinated with NanoSTING-S when challenged with the Delta VOC were protected in the lung against heterologous VOC and partially protected in the nasal passage. The reduction in viral loads in the nasal compartment suggests an advantage of mucosal vaccination to reduce transmission of the virus44.
Modeling of the immune response against both S- and N- proteins predicts synergistic protection

The results from the NanoSTING-S experiments demonstrated that the immune responses protect against disease in the lung but are insufficient to eliminate viral infection/replication in the nasal passage as a surrogate for transmission. To further bolster the protection against viruses, we explored additional antigens. We specifically chose the N protein because it is an abundantly expressed soluble and immunogenic protein. A mathematical model was used to help understand if a multi-antigen vaccine comprising both S- and N-proteins (NanoSTING-SN) can offer improved protection45. We explored the parameter space of an established model describing viral kinetics in the nasal passage obtained by fitting longitudinal viral titers from infected patients (Fig. 2A)46. The vaccine-induced neutralizing antibody responses against the S-protein serve as de-novo blockers of viral entry and impede viral production through immune effector mechanisms. We modeled a range (40–100%) of vaccine efficacies (directed only against the S-protein) to account for the differences in protection, specifically in the nasal compartment, and investigated the influence on viral elimination. The model revealed a reduction in viral load between 35% and 90% when the S-vaccine efficacy in the nasal compartment varied from 40 to 80% (Fig. 2B). An anti-S efficacy of  >80% in the nasal compartment is difficult to accomplish even with mucosal immunization (some IM vaccines offer no significant nasal immunity). Hence, it can explain the inability of vaccines targeting only the S protein to prevent nasal replication8,9. Next, we modeled a mucosal vaccine based exclusively on the N-protein. For the mucosal N-protein vaccine, we anchored to a mechanism of protection through the induction of cytotoxic T-cell responses that kill virally infected cells, thus reducing the number of cells capable of producing/propagating the virus. Under this scenario, the model predicted that the killing rate constant of cytotoxic T cells (CTL) would have to be 8.5 per day to achieve a 99% reduction in viral loads (Fig. 2C). This value is at least 10-fold higher than the predicted/measured killing capacity of CD8+ T cells in vivo; hence, it is not surprising that single-antigen N-based vaccines do not confer protection47,48. To quantify if multi-antigen vaccines can offer synergistic protection, we modeled combined protection by including S-directed vaccines that offer partial protection (primarily antibody-mediated) in the nasal compartment with the cytotoxic T-cell responses against the N protein. We tested a range of S-protein vaccine efficacies (40–100%) in the nasal compartment in combination with cytotoxic N responses (Fig. 2D). The model predicted that a physiologically relevant CTL killing rate of 0.4 and 0.6 days per day would lead to a 1000- and 10,000-fold reduction in peak viral load, respectively, when the efficacy of the spike vaccine was only 80% [Fig. 2D (red box) and Supplementary Fig. 5]. Indeed, studies in humans infected with COVID-19 have demonstrated a robust and long-lived CTL response in the nasal compartment and that CD8+ T cells specific for the N protein can directly inhibit viral replication49,50. Collectively, these results from modeling predicted that combination vaccines targeting S and N proteins can mediate synergistic protection in eliminating viral replication in the nasal compartment.
Fig. 2: Quantitative modeling of the combined immune response against both proteins predict synergistic protection.
figure 2

A Schematic and governing equations describing viral dynamics without vaccination, with spike protein immunization, or nucleocapsid protein immunization (IFNAR interferon-α/β receptor, IFN1 type-I interferons, ISG interferon-stimulated gene). In the nasal compartment, SARS-CoV-2 (V) infects target epithelial cells (T) at the rate βV. The infected cells remain in an eclipse phase (E) before they become infected cells (I) with a rate constant (k) and start producing viral particles at rate π. The infected cells produce antiviral responses, which make the target cells refractory (R) with a rate constant directly proportional to the number of infected cells (ɸI). The infected cells die with a rate constant (σ). The refractory cells become target cells at rate (ρ). B Upon immunization with spike protein, the rate constant of target cell infection is reduced from βV to βV(1-γ) where γ is antibody-mediated blocking efficiency. The bar graph shows a percent reduction in viral area under the curve (AUC) with increasing de-novo blocking efficiency (antibodies against the spike protein). C Upon immunization with N protein, the rate constant of elimination of infected cells is increased by ω due to the killing of infected cells by T cells. The bar graph shows a percent reduction in viral AUC upon cytotoxic T cell-mediated killing of infected cells. D Upon immunization with N and S protein the rate constant of elimination of infected cells is increased by ω and the rate constant of target cell infection is reduced from βV to βV(1-γ). The heatmap shows the effectiveness of the combined effect of de-novo blocking (S response) and T cell-mediated killing (N response). The red box indicates the synergistic effect of N and S response in achieving multifactorial immunity. See also Supplementary Fig. 5, Supplementary Methods, Sup Note 1. Parts of (A–D) were created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations - ACE2 angiotensin-converting enzyme 2, ISG interferon-stimulated gene, IFN1 type-I interferons, IFNAR interferon-α/β receptor, AUC area under the curve. Source data are provided as a Source Data file.
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Immunization with NanoSTING-SN vaccine yields balanced humoral and cellular immunity and eliminates virus in the lung and nasal compartments upon challenge with the SARS-CoV-2 Delta VOC

We formulated vaccines containing both antigens to test the model that the immune response against both the S and N proteins can be synergistic (Fig. 3A). We initially performed immunogenicity experiments in mice with 10 µg of each recombinant N and S proteins adjuvanted with NanoSTING. We observed that while 100% of animals seroconverted and showed IgG responses against the S protein, seroconversion against the N protein was variable (40–80%) [not shown]. We accordingly modified the mass ratio of N:S protein (2:1) and adjuvanted it with NanoSTING to formulate NanoSTING-SN (Fig. 3A). The NanoSTING-SN displayed a mean particle diameter of 142 nm (PDI 26.2%) and a mean zeta potential of −48.4 mV (Supplementary Fig. 6A, B). We tested NanoSTING-SN after 9 months of storage at 4 °C, and confirmed that it displayed excellent stability, like the NanoSTING-S vaccine (Supplementary Fig. 6C, D). Single-dose intranasal vaccination in mice with NanoSTING-SN was safe (Supplementary Fig. 7) and yielded robust serum IgG titers against the N protein and full-length S protein variants at day 35 (Fig. 3B). We documented robust antigen-specific, cross-reactive IgG responses in the BALF (Fig. 3C) and observed cross-reactive IgA responses in the serum and BALF at day 35 (Fig. 3D, E). We measured Th1 and Th2 responses against the N- and S- proteins in both the spleen and the lung at day 51 (Fig. 3F, G) and observed no significant Th2 response (IL4) in both tissues. Based on these promising immunogenicity data in mice, we evaluated the protective efficacy of NanoSTING-SN in hamsters. We vaccinated hamsters intranasally with two doses of NanoSTING-SN and challenged the immunized hamsters with the Delta VOC through the intranasal route (Fig. 3H). Animals immunized with NanoSTING-SN were completely protected from weight loss (mean peak weight loss of 1 ± 1%) [Fig. 3I]. Like the results of the NanoSTING-S vaccine, NanoSTING-SN eliminated viral replication in the lung by day 6 post-challenge (Fig. 3J), suggesting that S-specific immune responses are the dominant factor in providing immunity in the lung. In the nasal compartment, NanoSTING-SN showed a significant reduction in infectious viral particles by day 2, even in comparison to NanoSTING-S, and significantly, by day 6 there was a complete elimination of infectious viral particles in the nasal tissue of the NanoSTING-SN vaccinated animals (Fig. 3K). Pathology also confirmed that vaccinated and challenged animals had minimal alveolar damage (Fig. 3L, M). Although the resolution of the inflammatory responses characterized by macrophages and lymphocytes was different when comparing NanoSTING-SN (multiple antigens) vs NanoSTING-S (single antigen) (Figs. 3M, 1N), viral titers in both the lung and nasal compartments were eliminated upon vaccination with NanoSTING-SN. In aggregate, these results illustrate that NanoSTING-SN can provide complete elimination of the virus in both the lung and nasal compartments.
Fig. 3: NanoSTING-SN vaccine yields balanced humoral and cellular immunity targeting both proteins and eliminates virus in both the lung and nasal compartments upon challenge with the SARS-CoV-2 Delta VOC.
figure 3

A Experimental setup: We immunized two groups (n = 5/group) of mice by intranasal administration with NanoSTING-SN followed by serum collection every week. We monitored the body weights of the animals every week after the immunization until the end of the study. We euthanized the animals at day 51 followed by the collection of BALF, serum, lungs, and spleen. Body weight change, ELISA (IgG & IgA), and ELISPOT (IFNγ and IL4) were primary endpoints. Naïve BALB/c mice were used as controls (n = 5/group). B–E Humoral immune responses in the serum and BALF were evaluated using S-protein and N-protein based IgG & IgA ELISA. Splenocytes (F) or lung cells (G) were stimulated ex vivo with overlapping peptide pools, and IFNγ & IL4 responses were detected using an ELISPOT assay. H Timeline for challenge study done in Syrian golden hamsters: We immunized hamsters intranasally with two doses of NanoSTING-SN (first dose at day -42 and the second dose at day -18) and challenged the hamsters intranasally with 3 × 104 CCID50 of the SARS-CoV-2 Delta VOC on day 0. Post-challenge, we monitored the animals for 6 days for changes in their body weight. We euthanized half of the hamsters on day 2 and the other half on day 6 for histopathology of the lungs, with viral titers of lung and nasal tissues measured on day 2 and day 6. I Percent body weight change of hamsters compared to the baseline at the indicated time intervals. J, K Viral titers were measured by end-point titration assay in lungs and nasal tissues post-day 2 and day 6 of infection. The dotted line indicates LOD. L, M A representative hematoxylin and eosin (H & E) image and pathology scores of the lung showing histopathological changes in hamsters treated with NanoSTING-SN and PBS; all images were acquired at 10x & 20×; scale bar, 100 µm. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse/hamster. For (B–G, J, K, M), the analysis was performed using a two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns: not significant. For (I), the data was compared via mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. For (I), the exact p values comparing the NanoSTING-SN group to the PBS group are Day 2: p = 1.9e-2, Day 3: p = 1.0e-2, Day 4: p = 2.0e-2, Day 5: p = 7.3e-5, Day 6: p = 1.3e-5. Asterisks indicate significance compared to the PBS-treated animals at each time point. Data presented as combined results from two independent experiments [A–G: Immunogenicity study with NanoSTING-SN, H–M: Challenge study with Delta VOC], each involving one independent animal experiment. Gender was not tested as a variable, and only female mice were included in the study (A–G). Gender was tested as a variable with equal number of male and female hamsters included in the study (H–M). See also Supplementary Figs. 6, 7. A, H were created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations: IN Intranasal. Number of animals used: A–G: n = 4–5/group, H–M: n = 10/group Source data are provided as a Source Data file.
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Immunization with NanoSTING-N yields durable humoral and cellular immunity but is not sufficient to confer protection against Delta VOC

To quantify the role of anti-N immunity in mucosal protection, we characterized the immune response elicited against the N protein by formulating NanoSTING-N (NanoSTING-Nucleocapsid) and testing it in mice. Independent studies with K18-hACE2 mice immunized with viral vector-based N protein and challenged the early lineage variants (Wuhan and Alpha VOC) revealed mixed results with either partial or a complete lack of protection24,31. The predicted structure of the SARS-CoV-2 N protein comprises an RNA binding domain, a C-terminal dimerization domain, and three intrinsically disordered domains that promote phase separation with nucleic acids51 (Supplementary Fig. 8A). To confirm the size of the N-protein, we performed SDS-PAGE, wherein we demonstrated that the recombinant N protein had an estimated molecular mass of 47 kD (Supplementary Fig. 8B). We confirmed the functional activity of the protein by assaying binding to plasmid DNA based on the quenching of the fluorescent DNA condensation probe DiYO-1 (Supplementary Fig. 8C)52 with PEI (R) used as a positive control (Supplementary Fig. 8D). To formulate the vaccine, NanoSTING-N, we mixed the N protein with NanoSTING to allow the adsorption of the protein onto the liposomes (Fig. 4A). The formulated NanoSTING-N had a mean particle diameter of 107 nm (PDI 20.6%), and a mean zeta potential of −51 mV (Supplementary Fig. 8E, F). Although the recombinant N protein showed a strong propensity for aggregation upon storage at 4 °C for 6 months, NanoSTING-N was stable with no change in size or zeta potential (Supplementary Fig. 8G, H). Consistent with our NanoSTING-SN studies, we immunized two groups of mice by intranasal administration with either 10 µg (NanoSTING-N10) or 20 µg of N protein (NanoSTING-N20, Fig. 4A and Supplementary Fig. 9). The serum IgG responses at both doses were similar at day 27, although the IgG titers elicited by the NanoSTING-N20 were higher than NanoSTING-N10, the difference was not significant (Fig. 4B).
Fig. 4: NanoSTING-N vaccine yields durable humoral and cellular immunity in mice but is insufficient to confer protection against the highly infectious Delta VOC in hamsters.
figure 4

A Experimental setup: We immunized two groups (n = 5–6/group) of mice by intranasal administration with NanoSTING-N10 or NanoSTING-N20 followed by serum collection every week. We monitored the body weights of the animals every week after the immunization until the end of the study. We euthanized the animals at day 27 and then collected BALF, serum, lungs, and spleen. Body weight change, ELISA (IgG & IgA), flow cytometry (CD8+ T cells), and ELISPOT (IFNγ and IL4) were used as primary endpoints. Naïve BALB/c mice were used as controls (n = 4/group). B, C Humoral immune responses in the serum and BALF were evaluated using N-protein-based IgG ELISA. D Humoral immune responses in the serum were evaluated using N-protein-based IgA ELISA. Splenic CD8+ T cells were stimulated ex vivo with overlapping peptide pools, and (E, F) CD137 expression was quantified by flow cytometry (G) IFNγ & IL4 responses were detected using an ELISPOT assay. Splenic CD8+ T cells were stimulated ex vivo with overlapping peptide pools, and (H, I) GzB expression was quantified by flow cytometry (J) IFNγ & IL4 ESLIPOT from lung cells stimulated ex vivo with indicated peptide pools. K Experimental setup for challenge studies in Syrian golden hamsters. We immunized hamsters (n = 10/group) intranasally with two doses of NanoSTING-N (first dose at day -42 and the second dose at day -18 and challenged the hamsters intranasally with 3 × 104 CCID50 of the SARS-CoV-2 Delta VOC on day 0. Post-challenge, we monitored the animals for 6 days for changes in body weight. We euthanized half of the hamsters on day 2 and the other half on day 6 for histopathology of the lungs, with viral titers of lung and nasal tissues measured on day 2 and day 6. L Percent body weight change of hamsters compared to the baseline at the indicated time intervals. M, N Viral titers were measured by end-point titration assay in lungs and nasal tissues post-day 2 and day 6 of infection. The dotted line indicates LOD. O, P Pathology score and a representative H & E image of the lung showing histopathological changes in hamsters treated with NanoSTING-N and PBS; all images were acquired at 10x & 20×; scale bar, 100 µm. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse/hamster. For (B–G, J, K, M), the analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns: not significant. For (I), the data was compared via mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. Asterisks indicate significance compared to the PBS-treated animals at each time point. Data presented as combined results from two independent experiments [A–J: Immunogenicity study with NanoSTING-N, K–P: Challenge study with Delta VOC)], each involving one independent animal experiment. Gender was not tested as a variable for the study, and only female mice were used (A–G). Gender was tested as a variable with an equal number of male and female hamsters included in the study (H–M). See also Supplementary Figs. 8–12. A, K were created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations: GzB Granzyme, IN intranasal, N10 NanoSTING with 10 µg of Nucleocapsid protein, N20 NanoSTING with 10 µg of Nucleocapsid protein. Number of animals used: A–J: n = 4–6/group, K–P: n = 10/group Source data are provided as a Source Data file.
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In contrast to vaccination with the trimeric NanoSTING-S (early response at day 7), the kinetics of IgG responses were delayed, and responses were only observed at day 14 (Supplementary Fig. 10). Both, NanoSTING-N10 and NanoSTING-N20 yielded antigen-specific IgG responses in the BALF and IgA response in serum (Fig. 4C, D). We examined the activation and function of N-protein-specific memory CD8+ T cells in the lungs and spleen using granzyme B (GzB) and the activation-induced marker CD137. Restimulation ex vivo with a pool of overlapping peptides derived from the N protein resulted in a significant increase in the frequency of activated (CD8+CD137+), and cytotoxic (CD8+GzB+) T cells in the spleen (Fig. 4E, F, H, I) and to a lesser extent in the lung of both the NanoSTING-N10 and NanoSTING-N20 vaccinated mice (Supplementary Fig. 11B, C). The overall frequencies of the lung resident memory CD8+CD103+ and CD8+CD103+CD69+ T cells were no different between the immunized animals and the control group (Supplementary Fig. 11D, E). NanoSTING-N10 and NanoSTING-N20 immunized mice showed robust and significant splenic and lung Th1/Tc1 responses (Fig. 4G, J). We did not observe a measurable IL4 (Th2) response upon immunization with NanoSTING-N10 and NanoSTING-N20 (Fig. 4G, J). To test the durability of the NanoSTING-N response, we immunized mice with NanoSTING-N20 and monitored the animals for 62 days (Supplementary Fig. 12A). NanoSTING-N20 vaccinated animals reported no weight loss (Supplementary Fig. 12B) and revealed robust serum IgG and IgA titers at day 62 (Supplementary Fig. 12C, D). We also confirmed that the N-reactive Th1 responses were conserved in the spleen and lung at day 62 (Supplementary Fig. 12E, F). These results can be Collectively, these results establish that immunization with NanoSTING-N results in IgG and IgA immune responses and long-lived Th1/Tc1 but not deleterious Th2 immune responses.

Based on the immunogenicity data in mice, we evaluated the protective efficacy of NanoSTING-N in hamsters. We intranasally vaccinated hamsters with two doses of NanoSTING-N and challenged the immunized hamsters with the SARS CoV-2 Delta VOC through the intranasal route (Fig. 4K). Animals in both the vaccinated and sham-vaccinated groups showed significant weight loss (Fig. 4L). Consistent with the lack of protection from weight loss, infectious viral titers were no different in the lung or nasal passage on either day 2 or day 6 in both vaccinated and sham-vaccinated animals (Fig. 4M, N). In addition, we observed that the aggregate pathology score of NanoSTING-N treated hamsters was not significantly different from sham-vaccinated animals, although the distribution of pathology scores appeared bimodal (Fig. 4O, P). Collectively, the immunization and the challenge data are aligned with our mathematical model and illustrate that while NanoSTING-N elicits strong Tc1 responses, these responses are insufficient to prevent viral expansion in the absence of S-directed immunity.
Two doses of NanoSTING-SN abolishes transmission of SARS-CoV-2 Omicron VOC

The SARS-CoV-2 Omicron VOCs are transmitted very efficiently, and we next wanted to directly investigate if immunization with NanoSTING-SN can prevent the transmission of this highly infectious VOC. We established a transmission experiment using the SARS-CoV-2 Omicron VOC (BA.5) and two groups of Syrian golden hamsters. For group 1, the animals were sham immunized with PBS whereas for group 2, the animals were immunized with two doses NanoSTING-SN spaced by 21 days. These hamsters were challenged on day 35 with SARS-CoV-2 Omicron VOC (BA.5) and 1 day after the challenge; each animal was paired with a naïve unimmunized hamster (contact hamster) that allowed not only aerosol but also direct contact and fomite (including diet and bedding) transmission for 4 days (Fig. 5A). We quantified the viral titers in the index and contact hamsters in the lungs and nasal tissue. Vaccination protected the index hamsters from the virus, with only 2/8 hamsters showing a low amount of detectable virus in the lung (Fig. 5B) and nasal tissue (Fig. 5D). Vaccination completely blocked transmission in the lungs (Fig. 5C) and nasal tissue (Fig. 5E), and none of the contact hamsters showed detectable virus. These results suggest that at least early after immunization, two doses of NanoSTING-SN can prevent transmission of highly transmissible variants and long-term studies are warranted to quantify the duration of this protection.
Fig. 5: Intranasal vaccination with NanoSTING-SN abolishes transmission of SARS-CoV-2 Omicron (BA.5) VOC in hamsters.
figure 5

A Experimental setup: We immunized hamsters with a dual dose of the intranasal NanoSTING-SN vaccine (n = 10/group) or PBS (n = 8/group) 5 weeks (day-21) and 2 weeks (Day 0) prior to infection with ∼3 × 104 CCID50 of SARS-CoV-2 Omicron VOC (BA.5) [Day 14]. One day after the viral challenge, we co-housed the index hamsters in pairs with contact hamsters for 4 days in clean cages. We euthanized the index hamsters on day 4 of cohousing and contact hamsters on day 5 of cohousing. Viral titers in the lungs of the index and contact hamsters were used as primary endpoints. B, C Infectious viral particles in the lung tissue of contact and index hamsters at day 5 after viral administration post-infection were measured by end-point titration assay. The dotted line indicates LOD. D, E Infectious viral particles in the nasal tissue of contact and index hamsters at day 5 after viral administration post-infection were measured by end-point titration assay. The dotted line indicates LOD. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual hamster. The analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Asterisks indicate significance compared to the PBS-treated animals at each time point. Data presented as combined results from one independent experiment. Gender was tested as a variable, and an equal number of male and female hamsters were included in the study. A and parts of (B–E) were created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Number of animals used: n = 8–10/group Source data are provided as a Source Data file.
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VanLaraklios

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Re: Team develops 2 nasal sprays to prevent virus transmission
« Reply #4 on: August 07, 2024, 09:30:49 PM »


We repeated these studies with a single dose of the vaccine and challenged with the SARS-CoV-2 Omicron VOC (BA.1.1.529). Even a single dose of the vaccine significantly reduced transmission to naïve animals (Fig. 6). These results demonstrated that even a single dose of NanoSTING-SN is effective at mitigating the transmission of the Omicron VOC, and two doses of the vaccine were sufficient to eliminate transmission, which has implications for controlling the outbreak of respiratory pathogens.
Fig. 6: Single dose intranasal administration of NanoSTING-SN limits transmission and viral replication of SARS-CoV-2 Omicron (B.1.1.529) VOC in hamsters.
figure 6

A Experimental setup: We immunized hamsters with a single dose of the intranasal NanoSTING-SN (n = 10/group) vaccine or PBS (n = 8/group) 3 weeks prior to infection with ∼3 × 104 CCID50 of SARS-CoV-2 Omicron VOC (B.1.1.529). One day after the viral challenge, we co-housed the index hamsters in pairs with contact hamsters for 4 days in clean cages. We euthanized the contact and index hamsters on day 4 of cohousing. Viral titers in the nasal tissue of the index and contact hamsters were used as primary endpoints. B, C Infectious viral particles in the nasal tissue of contact and index hamsters at day 5 after viral administration post-infection were measured by end point titration assay. The dotted line indicates LOD. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual hamster. The analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Asterisks indicate significance compared to the PBS-treated animals at each time point. Data presented as combined results from one independent experiment. Gender was tested as a variable with an equal number of male and female hamsters included in study. A and parts of (B, C): Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations: d2 Day 2, d5 Day 5, IN Intranasal. Number of animals used: n = 8–10/group. Source data are provided as a Source Data file.
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NanoSTING-SN yields cross-reactive humoral immunity and confers protection against SARS-CoV

We next wanted to assess whether immunization with NanoSTING-SN would yield humoral responses that are cross-reactive against coronaviruses. Although the trimeric spike proteins from SARS-CoV, SARS-CoV-2, and MERS-CoV are structurally similar (Fig. 7A), sequence alignment of the RBDs of these same proteins showed significant sequence divergence (Fig. 7B). We evaluated the efficacy of NanoSTING-SN in mice by assaying the immune sera against both full-length S and N proteins and the RBDs from SARS-CoV-2, SARS-CoV, MERS-CoV (betacoronavirus) and HCOV-229E (alphacoronavirus) [Supplementary Fig. 13], with the RBD reactivity serving as a surrogate for neutralization. We documented robust antigen-specific, cross-reactive IgG responses against full-length S proteins and, as anticipated by the sequence divergence, a reduction in the reactivity to the RBDs of these different coronaviruses (Fig. 7C, D). By contrast, serum IgG ELISA against N proteins revealed similar titers against SARS-CoV-2 and SARS-CoV N proteins (Fig. 7C).
Fig. 7: Immunization of mice with NanoSTING-SN vaccine yields cross-reactive humoral immunity against betacoronaviruses and confers protection against SARS-CoV.
figure 7

A 3D structure of SARS-CoV-2, SARS-CoV, and MERS-CoV spike proteins showing binding to respective receptors (PDB: 6ZP7, 5X5B, 5X5C). B Multiple sequence alignment of RBDs of SARS-CoV-2, SARS-CoV, and MERS-CoV spike (S) proteins. GenBank accession numbers are QHR63250.1 (SARS-CoV-2 S), AY278488.2 (SARS-CoV S), and AFS88936.1 (MERS-CoV S). C, D Humoral immune responses in the serum were evaluated using N and S protein-based IgG ELISA. E Experimental set up for SARS-CoV challenge studies in mice. We immunized mice (n = 10/group) intranasally with one dose of NanoSTING-SN on day 0 and a second dose on day 21 and challenged the mice intranasally with the SARS-CoV (v2163 strain) on day 35. Post-challenge, we monitored the animals for 14 days for changes in body weight and survival. F Percent body weight change of mice compared to the baseline at the indicated time intervals. G Percent survival of mice compared to the baseline at the indicated time intervals. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bars representing SEM. Each dot represents an individual mouse. For (C, D), the analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. For (F), the data was compared via mixed-effects model for repeated measures analysis. Lines depict group mean body weight change from day 0; error bars represent SEM. For (F), the exact p values comparing the NanoSTING-SN group to the Placebo group are Day 3: p = 2.7e-7, Day 4: p = 1.9e-10, Day 5: p = 7.1e-12, Day 6: p < 1.0e-15, Day 7: p = 2.9e-13, Day 8: p = 1.2e-8, Day 9: p = 3.8e-4, Day 10: p = 8.0e-3, Day 11: p = 9.3e-3, Day 12: p = 2.2e-2, Day 13: p = 3.3e-2, Day 14: p = 7.4e-3. Asterisks indicate significance compared to the PBS-treated animals at each time point. For (G), we compared survival percentages between NanoSTING-SN and PBS-treated animals using the Log-Rank Test (Mantel-Cox). Data presented as combined results from two independent experiments [C, D: Immunogenicity study with NanoSTING-SN, E–G: Challenge study with SARS-COV], each involving one independent animal experiment. Gender was not tested as a variable, and only female mice were used for the study (C, D). Gender was tested as a variable with an equal number of male and female mice included in the study (E–G). See also Supplementary Figs. 13, 14. E Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations: ACE2 angiotensin-converting enzyme 2, D35 Day 35, IN Intranasal. Number of animals used: C, D: n = 4–5/group, E–G: n = 10/group Source data are provided as a Source Data file.
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To test if the cross-reactive humoral activity against the S-RBD translated to protection against viral challenge, we tested the efficacy of dual dose intranasal NanoSTING-SN in mice against SARS-CoV (v2163 strain) [Fig. 7E]. Upon challenge with SARS-CoV, mice in the sham-vaccinated group showed a mean peak weight loss of 27 ± 1%. By contrast, animals vaccinated with NanoSTING-SN showed completely normal weights that were no different from unchallenged animals at all indicated time points (Fig. 7F). Survival data confirmed that NanoSTING-SN vaccinated mice showed 100% survival, illustrating a significant impact of treatment on survival of mice compared to the PBS group (Fig. 7G). These results demonstrated that NanoSTING-SN can provide complete protection against challenge from multiple sarbecoviruses.

Since our data with SARS-CoV-2 (Figs. 1J, 3I) illustrated that immune response against the spike protein elicited by NanoSTING-S was sufficient to protect the animals from weight loss, we investigated if the dominant protection afforded by NanoSTING-S would also translate to SARS-CoV. As expected, animals immunized with two doses of NanoSTING-S and NanoSTING-SN (Supplementary Fig. 14A) showed completely normal weights and 100% survival as compared to PBS-treated animals (Supplementary Fig. 14B, C).
NanoSTING-SN confers durable humoral immunity in rhesus macaques

To assess the efficacy of NanoSTING-SN on Rhesus macaques (M. mulatta), we immunized three animals intranasally with two doses of NanoSTING-SN on Day 0 and Day 28 (booster dose). We monitored the animals for 44 days to track changes in body weight, attitude, appetite, and body temperature (Fig. 8A). None of the animals showed clinical signs such as loss of body weight (Fig. 8B) or increase in body temperature (Fig. 8C) upon administration of NanoSTING-SN. We evaluated humoral immunity induced in rhesus macaques using SARS-CoV-2 spike and nucleoprotein-specific IgG ELISA. We evaluated the efficacy of the dual dose of NanoSTING-SN by assaying the immune sera collected at day 21 and day 45 against both full-length S and N proteins and RBD from SARS-CoV-2 variants (BA.1, XBB1.5), SARS-CoV, and MERS-CoV. Consistent with our mice data, we documented robust antigen-specific, cross-reactive IgG responses against full-length S & N proteins from SARS-CoV-2 variants and from other coronaviruses at day 21 and post booster, the IgG titers were significantly increased at day 45 (Fig. 8D, E). Importantly, the IgG responses against both the S and N proteins did not reduce significantly over 6 months in the immunized NHPs (Non-human primates) (Supplementary Fig. 15).
Fig. 8: NanoSTING-SN confers durable humoral immunity in rhesus macaques.
figure 8

A Experimental setup: We administered two doses of the intranasal NanoSTING-SN vaccine (n = 3/group) 28 days apart to rhesus macaques. We collected the sera on days 0, 7, 14, 28, and 44 to evaluate humoral immune responses. We monitored the body weights of the animals every week after the immunization until the end of the study. Body weight change, body temperature change, and ELISA (IgG & IgA) were used as primary endpoints. Pre-immunization sera was used as control. B Percent body weights change for the non-human primates. C Body temperature changes for the non-human primates. D, E Humoral immune responses in the serum were evaluated using N and S protein-based IgG ELISA. F, G Humoral immune responses in the serum were evaluated using N and S protein-based IgA ELISA. H Humoral immune responses in the nasal washes were evaluated using N and S protein-based IgA ELISA. Individual data points represent independent biological replicates taken from separate animals; vertical bars show mean values with error bar representing SEM. Each dot represents an individual animal. For (D–H), the analysis was performed using two-tailed Mann-Whitney U-test: ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05; ns not significant. Data presented as combined results from one independent experiment. Two male and one female NHPs were used for the study. See also Supplementary Fig. 15. A Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en). Abbreviations: IN Intranasal. Number of animals used: n = 3/group Source data are provided as a Source Data file.
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To test mucosal immunity, we evaluated IgA responses after both the prime and the boost immunizations. We detected elevated cross-reactive serum IgA responses against full-length N, RBD, and all spike protein variants tested from SARS-CoV-2, SARS-CoV, and MERS (Fig. 8F, G). In humans, although serum IgG levels were associated with the prevention of disease against SARS-CoV-2 variants, newer data suggest that IgA antibodies in the nasal compartment correlate strongly with protection against infection, especially against the Omicron VOCs, and may serve as a surrogate for protection53,54. Accordingly, we evaluated the nasal wash IgA titers elicited upon immunization of the NHPs with NanoSTING-SN. We measured detectable and significant IgA responses against the S and N proteins of SARS-CoV-2 and the S protein of MERS-CoV (Fig. 8H). These results illustrate that NanoSTING-SN elicits cross-reactive mucosal responses in the nasal compartment of rhesus macaques.
Discussion

The continued evolution of SARS-CoV-2 and the potential for recombination between SARS-CoV-2 and closely related coronaviruses in bats has prompted an urgency in the development of vaccines targeting sarbecoviruses and coronaviruses55,56. Our study makes an essential contribution to the next-generation of pan-sarbecovirus and coronavirus vaccines. In this context, we report four significant results with NanoSTING-SN: (1) it yields both mucosal and systemic immunity against SARS-CoV-2 in hamsters against Delta VOC challenge, (2) it was sufficient to completely block transmission of the highly transmissible Omicron VOC (BA.5) to vaccine-naïve hamsters, (3) it confers complete protection against SARS-CoV in mice, and (4) it elicits cross-reactivity Ig responses in both the serum and nasal compartment of NHPs.

Several next-generation SARS-CoV-2 and pan-sarbecovirus vaccines have been developed and these can be classified into three categories: (1) intranasal vaccines, (2) pan-sarbecovirus vaccines, and (3) dual-antigen vaccines, recognizing that the categories can be overlapping. Intranasal (and oral) vaccines for SARS-CoV-2 have been developed and translated to humans57,58. The vaccine based on a viral vector expressing the Wuhan S protein (ChAd-SARS-CoV-2-S) showed results similar to NanoSTING-S, demonstrating reduction but also variability in viral loads in the upper airways of K18-hACE2 mice challenged with chimeric viruses with spike genes corresponding to SARS-CoV-2 VOC (B.1.351 and B.1.1.28)59. Another vaccine candidate based on adenovirus type 5–vectored SARS-CoV-2 Wuhan S protein was tested both using intranasal and oral administration, and both routes yielded only modest reduction in viral titers in hamsters57. The vaccine candidate was also tested in humans, but the program was subsequently abandoned57. A “prime and spike” vaccine (IM vaccination with the mRNA and an intranasal boost with the unadjuvanted Wuhan SARS-CoV-2 spike protein) showed efficacy comparable to dual dose mRNA vaccines against the ancestral SARS-CoV-2 (2020/USA-WA1) strain in mice: reduction (but not elimination) of viral titers in the lung and nostrils, and protection from weight loss in mouse models60. In a hamster transmission model, even a brief 4 h cohousing with an infected animal, allowed dual-dose vaccinated animals to pick up the infection. Although the vaccine was durable (challenge was performed 118 days after immunization), the efficacy was not tested against multiple strains of SARS-CoV-2, and protection against SARS-CoV required boosting with the intranasal spike derived from SARS-CoV60. From a vaccination perspective, having to continuously change the spike protein entails manufacturing of new proteins and, hence, is not scalable/translatable.

Pan-sarbecovirus vaccines designed based on either chimeric S proteins (mRNA based) or RBD-nanoparticles (protein-based) have been tested preclinically61,62. The S protein of sarbecoviruses comprises of three immunogenic domains: the N-terminal domain (NTD), the receptor binding domain (RBD), and the subunit 2 (S2). Synthetic chimeric S proteins constructed by varying the NTD/RBD/S2 from different sarbecovirus were formulated as nucleoside-modified mRNA vaccines encapsulated in lipid nanoparticles (mRNA-LNP)61. To further facilitate cross-reactivity, mixtures of four separate such chimeric spikes were included in the vaccine and were administered IM in a prime boost regimen. These chimeric vaccines showed protection against mouse adapted strains of SARS-CoV and SARS-CoV-2 (Beta VOC) with robust protection from weight loss61. The use of K18-hACE2 mice and the lethality of the viruses in this mouse model precludes transmission studies to quantify the impact of the vaccines on transmission. The dense and precise nanoscale organization of antigens is a feature of viruses considered essential for stimulating a robust humoral response63. The Spycatcher-spytag-based system leads to the display of 60mers of antigens, and this system was used to construct nanoparticles randomly displaying the RBDs of eight different sarbecoviruses (mosaic-8 RBD nanoparticles)62. Similar to the chimeric mRNA-LNPs described above, dual dose IM immunization of K18-hACE2 mice showed robust protection against weight loss when challenged with either SARS-CoV and SARS-CoV-2 (Beta) but formal transmission studies were not undertaken. Of note, the mosaic nanoparticles were tested in NHPs using a three-dose immunization regimen, and the vaccinated animals showed a ~100-fold reduction (but not elimination) of infectious virus in nasal swabs when challenged with the SARS-CoV-2 Delta VOC62. By contrast, dual dose immunization with NanoSTING-SN led to the complete elimination of the infectious virus in the nasal tissue in hamsters when challenged with the SARS-CoV-2 Delta VOC. Although the data are unavailable, intranasal immunization with mosaic-8 RBD nanoparticles adjuvanted with NanoSTING or even synthetic STING agonists like CF501 will provide an orthogonal formulation for pan-sarbecovirus vaccines64.

Dual antigen vaccines targeting both the S and N proteins have been tested as either mRNA-LNP formulations or adenoviral vector vaccines23,24. The dual mRNA vaccine was administered IM in two doses and was tested against both SARS-CoV-2 Delta and Omicron VOCs in hamsters23. Consistent with our studies, using the two antigens showed additive protection, but consistent with IM immunization, the mRNA vaccines could not eliminate the virus in the nostrils. The adenoviral vector vaccine engineered to express both the S and N proteins was administered IM and tested against challenge by SARS-CoV-2 (2020/USA-WA1) strain in K18-hACE2 mice24. Comparisons of the S-only and the dual antigen vaccine formulations showed that while the S vaccine was sufficient to provide immunity in the lung, protection of the nervous system and the brain was only observed with the dual antigen vaccine. These observations complement our results with NanoSTING-SN and further reinforce the importance of multi-protein vaccines.

The ability to elicit multifactorial immunity in the nasal cavity has several implications for the design of vaccines targeting respiratory viruses. First, since respiratory viruses like SARS-CoV-2 can access the brain through the olfactory mucosa in the nasal cavity, immunity in this compartment can prevent viral seeding to the brain. This, in turn, can prevent the entire spectrum of neurological complications ranging from the immediate loss of smell and taste to long-term complications like stroke65,66. Second, eliminating the virus in the nasal cavity of vaccinated recipients reduces the chance of viral evolution leading to breakthrough disease, especially in the context of waning immunity67. Allowing the virus to persist is a risky experiment in viral evolution with likely tragic consequences68. Eradicating the SARS-CoV-2 viral reservoir in humans provides the only reasonable path to moving past the pandemic and the perpetual cycle of repeated booster vaccinations. Third, as the recent human data with Omicron infection in vaccinated hosts illustrates the importance of mucosal immunity in preventing infection, and the identification of nasal antigen-specific IgA as a correlate of protection from infection helps the design of mucosal vaccines53,54,69.

History provides a powerful example of the importance of vaccination to prevent infections, not just disease, and sets a clinical precedent. Similar to the current COVID-19 commercial vaccines, the first inactivated polio vaccine in 1955 successfully prevented disease but not infection. The availability of the oral polio vaccine starting in 1960 paved the way for eliminating infection and eradicating polio. The availability of multi-antigen mucosal vaccines provides a pathway for humanity to move past SARS-CoV-2 outbreaks.

In summary, we have developed and validated a multi-component intranasal NanoSTING-SN subunit vaccine candidate that directly eliminates transmission of highly transmissible variants and protects against multiple sarbecoviruses.
Methods
Preparation of NanoSTING, NanoSTING-S, NanoSTING-N, and NanoSTING-SN

The liposomes contained DPPC, DPPG, Cholesterol (Chol), and DPPE-PEG2000 (Avanti Polar lipids) in a molar ratio of 10:1:1:1. To prepare the liposomes, we mixed the lipids in CH3OH and CHCl3. We used a vacuum rotary evaporator to evaporate them at 45 °C. We dried the resulting lipid thin film in a hood to remove residual organic solvent. Next, we added pre-warmed cGAMP (Medchem Express) solution (3 mg/mL in PBS buffer at pH 7.4) to hydrate the lipid film. We mixed the hydrated lipids for an additional 30 min at an elevated temperature of 65 °C and subjected them to freeze-thaw cycles. Using a Branson Sonicator (40 kHz), we next sonicated the mixture for 60 min and used Amicon Ultrafiltration units (MW cut off 10 kDa) to remove the free untrapped cGAMP. Finally, we used PBS buffer to wash the NanoSTING (liposomally encapsulated STINGa) three times. We measured the cGAMP concentration in the filtrates against a calibration curve of cGAMP at 260 nm using Take3 Micro-Volume absorbance analyzer of Cytation 5 (BioTek). We calculated the final concentration of cGAMP in NanoSTING and encapsulation efficiency by subtracting the concentration of free drug in the filtrate. To prepare NanoSTING adjuvanted subunit protein vaccine, we used a simple “mix and adsorb” approach. Briefly, (i) NanoSTING-S vaccine was prepared by gently mixing 10 µg of trimeric spike protein-B.1.351 (Acrobiosystems, #SPN-C52Hk) with 20 µg of NanoSTING. (ii) NanoSTING-N (Wuhan) (BEI, # NR-53797): Two different concentrations of the Nucleocapsid protein were taken: NanoSTING-N10 (10 µg of N protein) and NanoSTING-N20 (20 µg of N protein) were mixed separately with 20 µg of the NanoSTING. (iii) NanoSTING-N: 20 µg of nucleocapsid protein-B.1.17 (Acrobiosystems, #NUN-C52H8) was mixed with 20 µg of NanoSTING. (iv) NanoSTING-SN: 10 µg of trimeric spike protein-B.1.351 (Acrobiosystems, #SPN-C52Hk) and 20 µg of nucleocapsid protein-B.1.17 (Acrobiosystems, #NUN-C52H8) were mixed with 20 µg of NanoSTING. All the vaccines were left on ice for a minimum of 1 h with constant slow shaking on the rocker.
Stability studies for the formulated vaccines

We stored the NanoSTING, NanoSTING-S, NanoSTING-N, and NanoSTING-SN at 4 °C for 6–9 months to check their stability. We measured the average hydrodynamic diameter and zeta potential of NanoSTING and all vaccine formulations using DLS and zeta sizer on Litesizer 500 (Anton Paar).
Cell lines

THP-1 dualTM cells (NF-κB-SEAP IRF-Luc Reporter Monocytes) [InvivoGen, SanDiego, CA, thpd-nfis] were cultured in a humidified incubator at 37 °C and 5% CO2 and grown in RPMI 1640, 2 mM L-glutamine, 25 mM HEPES, 10% heat-inactivated fetal bovine serum, 100 μg/ml Normocin™, Pen-Strep (100 U/ml-100 μg/ml). THP-1 dual cells were grown in the presence of respective selection agents [100 mg/mL zeocin (InvivoGen, #ant-zn-1)] and 10 mg/mL blasticidin (InvivoGen, #ant-bl-1)] every other passage to maintain positive selection of reporters.
Cell stimulation experiments with luciferase reporter enzyme detection

We performed the THP-1 dual cell stimulation experiments using the manufacturer’s instructions (InvivoGen, CA, USA). First, we seeded the cells in 96 well plate at 1 × 105 cells/well in 180 μL growth media. We then incubated the cells with 5 µg of NanoSTING at 37 °C for 24 h. To detect IRF activity, we collected 10 μL of culture supernatant/well at 12 h and 24 h and transferred it to a white (opaque) 96 well plate. Next, we read the plate on Cytation 7 (Cytation 7, Bio-Tek Instruments, Inc.) after adding 50 μL QUANTI-Luc™ (InvivoGen) substrate solution per well, followed by immediate luminescence measurement, which was given as relative light units (RLU).
DNA binding assay

We performed the DNA binding studies as previously published52. To check the applicability of the assay for detecting DNA condensation, we used branched-chain PEI (Polyethylenimine) as a positive control (Sigma Chemical Co., St. Louis, MO # 408727). DiYO-1 (AAT Biorequest #17579) and plasmid (pMB75.6)-DNA were mixed in equal volumes (in 20 mM HEPES, 100 mM NaCl, pH = 7.4) to achieve a final concentration of 400 nM DNA phosphate and 8 nM DiYO-1, respectively. The solution was left at room temperature (RT) for 5 h before use. Next, we added PEI at different concentrations (R = 0, 1, 2, 5 where R is the molar ratio of PEI Nitrogen to DNA phosphate) to DNA-DiYO-1 solution, mixed for 1 min, and left for 2 h to equilibrate. We measured the fluorescence intensity of the solution at excitation and emission wavelengths of 470 nm and 510 nm, respectively. We repeated the same procedure with SARS-CoV-2 N protein instead of PEI. To the DNA-DiYO-1 solution, we added the N protein at concentrations of 0.1 µM and 0.5 µM.
Mice and immunization

All studies using animal experiments were reviewed and approved by the University of Houston (UH) IACUC. We purchased the female 7–9-week-old BALB/c mice from Charles River Laboratories (Strain code: 028). The mice were maintained within a Specific Pathogen Free (SPF) facility housed on ventilated racks within micro-isolation caging systems. Notably, the mice were not bred within the facility premises and were co-housed during the study. The housing facility for mice was under a 12:12-h light: dark cycle at temperatures 20–22 °C, humidity 40–50%. Before immunization, we anesthetized the groups of mice (n = 4–6/group) by intraperitoneal injection of ketamine (80 µg/g of body weight) and xylazine (6 µg/g of body weight). Then, we immunized the animals intranasally with (i) NanoSTING-S vaccine (ii) NanoSTING-N10 and NanoSTING-N20 (iii) NanoSTING-N (iv) NanoSTING-SN. All vaccines were freshly prepared.
Body weight monitoring and sample collection

We monitored the body weight of the animals every 7 days until the end of the study after immunization. In addition, we collected the sera every week post-vaccination to detect the humoral immune response. We kept the blood at 25 °C for 10 min to facilitate clotting and centrifuged it for 5 min at 2000 × g. We collected the sera, stored it at −80 °C, and used it for ELISA. We harvested BALF, nasal wash, lung, and spleen at the end of the study, essentially as previously described70,71. We kept the sera and other biological fluids [with protease inhibitors (Roche, #11836153001)] at −80 °C for long-term storage. After dissociation, the splenocytes and lung cells were frozen in FBS + 10% DMSO and stored in the liquid nitrogen vapor phase until further use.
Mouse ELISA

We determined the anti-N and anti-S antibody titers in serum or other biological fluids (BALF and nasal wash) using ELISA. Briefly, we coated 0.5 μg/ml S protein (α variant: Cat# NR-55311, BEI Resources, VA, USA; β variant: Cat# SPN-C52Hk, Acrobiosystems, DE, USA; γ variant: Cat# SPN-C52Hg, Acrobiosystems, δ variant: Cat# 10878-CV, R&D Systems, MN, USA; ο variant: Cat# SPN-C52Hz, Acrobiosystems) and 1 μg/ml N protein (Sino Biological, PA, USA) onto ELISA plates (Corning, NY, USA) in PBS overnight at 4 °C or for 2 h at 37 °C. The plate was then blocked with PBS + 1% BSA (Fisher Scientific, PA, USA) + 0.1% Tween 20TM (Sigma-Aldrich, MD, USA) for 2 h at RT. After washing, we added the samples at different dilutions. We detected the captured antibodies using HRP-conjugated anti-mouse IgG (Jackson ImmunoResearch Laboratories, 1 in 6,000; PA, USA) and goat anti-mouse IgA biotin (Southern Biotech, 1: 5000; AL, USA). Streptavidin-HRP (Vector Laboratories, 1 in 2500, CA, USA) was used to detect the anti-IgA biotin antibodies. For BALF IgG ELISAs, antigens were coated onto plates at 0.5 μg/ml (S protein) and 2 μg/ml (N protein). We obtained the positive controls (anti-N and anti-S IgG) from Abeomics (CA, USA). We conducted three individual studies (NanoSTING-S, NanoSTING-N, and NanoSTING-SN), each with its own distinct control sets. We collected sera from the control animals upon completion of each study. The threshold for positivity was set at an optical density (450 nm) value of 0.05 or two times the negative control (PBS), whichever was higher. Endpoint titers were defined as the lowest dilution that was higher than the threshold for positivity.
Mouse RBD ELISA

We evaluated RBD-specific serum IgG and IgA in mice using indirect ELISAs. We coated the plates with 0.5 μg/ml spike RBD proteins (α variant: Cat# NR-55277, BEI Resources, Manassas, VA; β variant: Cat# NR-55278, BEI Resources). We incubated the plates overnight at 4 °C or 2 h at 37 °C. The unbound protein was washed off by rinsing the wells twice with PBS + 0.05% Tween-20 (PBST). The remaining active protein binding sites on the plates were blocked off by incubating the plates with PBS + 1% BSA + 0.1% Tween-20 for 1 h at RT. After two additional washes with PBST, we added the serum samples serially diluted in PBST + 0.5% BSA. Endpoint titers were evaluated by adding serum samples in two-fold dilutions in duplicates. Following 1 h incubation with diluted serum, we washed the plates four times with PBST and added HRP-conjugated anti-mouse IgG (Cat# 115-035-166, Jackson ImmunoResearch Laboratories, 1: 5000; PA, USA) to detect RBD protein-specific IgG. To detect IgA in serum, we used Goat anti-mouse IgA biotin (Cat# 1040-05, Southern Biotech, 1: 5000; AL, USA). Streptavidin-HRP (Vector Laboratories, 1: 2500, CA, USA) was used to detect the anti-IgA biotin antibodies. We incubated the plates with detection antibodies for 1 h at room temperature. We washed the plates four times with PBST before adding 100 μl 1-Step™ TMB ELISA Substrate Solution (Cat# 34021, ThermoFisher, MA, USA). The plates were incubated with TMB for 30 min at room temperature, and we added 2 M H2SO4 to stop color development. Finally, we recorded optical density (OD) values using Cytation 7 (Biotek Instruments Inc).
Processing of spleen and lungs for ELISPOT and flow cytometry

To isolate lung cells, we perfused the lung vasculature with 5 ml of 1 mM EDTA in PBS without Ca2+, Mg2+ and injected it into the right cardiac ventricle. Each lung was cut into 100–300 mm2 pieces using a scalpel. We transferred the minced tissue to a tube containing 5 ml of digestion buffer containing collagenase D (2 mg/ml, Roche #11088858001) and DNase (0.125 mg/ml, Sigma #DN25) in 5 ml of RPMI for 1 h and 30 min at 37 °C in the water bath and vortexed after every 10 min. We disrupted the remaining intact tissue by passage (6–8 times) through a 21-gauge needle. Next, we added 500 µL of ice cold-stopping Buffer (1 × PBS, 0.1 M EDTA) to stop the reaction. We then removed tissue fragments and dead cells with a 40 µm disposable cell strainer (Falcon) and collected the cells after centrifugation at 400 × g. We then lysed the red blood cells (RBCs) by resuspending the cell pellet in 3 ml of ACK Lysing Buffer (Invitrogen) and incubated for 3 min at RT, followed by centrifugation at 400 × g. Then, we discarded the supernatants and resuspended the cell pellets in 5 ml of complete RPMI medium (Corning, NY, USA). Next, we collected the spleen in RPMI medium and homogenized them through a 40 µm cell strainer using the hard end of a syringe plunger. After that, we incubated splenocytes in 3 ml of ACK lysis buffer for 3 min at RT to remove RBCs, then passed through a 40 µm strainer to obtain a single-cell suspension. We counted the lung cells and splenocytes by the trypan blue exclusion method.
ELISPOT

IFNγ and IL4 ELISpot assay was performed using Mouse IFNγ ELISPOT basic kit (ALP) and Mouse IL4 ELISPOT basic kit following the manufacturer’s instructions (Mabtech, VA, USA). For cell activation control, we treated the cultures with 10 ng/ml phorbol 12-myristate 13-acetate (PMA) (Sigma, St. Louis, MI, USA) and 1 µg/ml of ionomycin (Sigma, St. Louis, MI, USA). We used the complete medium (RPMI supplemented with 10% FBS) as the negative control. We stimulated splenocytes and lung cells (3 × 105) in vitro with either N-protein peptide pool (Miltenyi Biotec; #130-126-699, Germany) or an S-protein peptide pool (Genscript, # RP30020, USA) or S-protein (B.1.351) mutation peptide pool (Miltenyi Biotec, # 130-127-958, Germany) at a concentration of 1.5 μg/ml/peptide at 37 °C for 16–18 h in pre-coated ELISpot plate (MSIPS4W10 from Millipore) coated with AN18 IFNγ (1 µg/ml, Mabtech #3321-3-250;) and 11B11 IL4 (1 µg/ml, Mabtech #3311-3-250) coating antibody. The next day, we washed off the cells and developed the plates using biotinylated R4-6A2 anti-IFN-γ (Mabtech #3321-6-250) and BVD6-24G2 anti-IL4 (Mabtech #3311-6-250) detection antibody, respectively. Then, we washed the wells and treated them for 1 h at RT with 1:30,000 diluted Extravidin-ALP conjugate (Sigma, St. Louis, MI, USA). After washing, we developed the spots by adding 70 µL/well of BCIP/NBT-plus substrate (Mabtech #3650-10) to the wells. We incubated the plate for 20–30 min for color development and washed it with water. We quantified the spots using Cytation 7 (Bio-Tek Instruments, Inc.). Each spot corresponds to an individual cytokine-secreting cell. We showed the values as the background-subtracted average of measured triplicates.
Cell surface staining, intracellular cytokine staining for flow cytometry

We stimulated the spleen and lung cells from immunized and control animals to detect nucleocapsid protein-specific CD8+ T cell responses with an N protein-peptide pool at a concentration of 1.5 μg/mL/peptide (Miltenyi Biotec; 130-126-699, Germany) at 37 °C for 16–18 h followed by the addition of Brefeldin A (5 μg/ml BD Biosciences #BD 555029) for the last 5 h of the incubation. We used 10 ng/ml PMA (Sigma, St. Louis, MI, USA) and 1 µg/ml ionomycin (Sigma, St. Louis, MI, USA) as the positive control. Stimulation without the peptides served as background control. We collected the cells and stained with Live/Dead Aqua (Thermo Fisher #L34965) in PBS, followed by Fc-receptor blockade with anti-CD16/CD32 (Thermo Fisher #14-0161-85), and then stained for 30 min on ice with the following antibodies in flow cytometry staining buffer (FACS): anti-CD4 AF589 (clone GK1.5; Biolegend #100446), anti-CD8b (clone YTS156.7.7; Biolegend #126609), anti-CD69 (clone H1.2F3; Biolegend #104537), anti-CD137 (clone 1AH2; BD; # 40364), anti-CD45 (clone 30-F11; BD; #564279). We washed the cells twice with the FACS buffer. We then fixed them with 100 μL IC (intracellular) fixation buffer (eBioscience) for 30 min at RT. We permeabilized the cells for 10 min with 200 μL permeabilization buffer (BD Cytofix solution kit). We performed the intracellular staining using the antibodies Alexa Fluor 488 interferon (IFN) gamma (clone XMG1.2; BD; #557735) and Granzyme B (clone GB11; Biolegend; #515407) overnight at 4 °C. Next, we washed the cells with FACS buffer and analyzed them on LSR-Fortessa flow cytometer (BD Bioscience) using FlowJo™ software version 10.8 (Tree Star Inc, Ashland, OR, USA). We calculated the results as the total number of cytokine-positive cells with background subtracted. We optimized the amount of the antibodies by titration. See Supplementary Fig. 11A for the gating strategy.
Viruses and biosafety

Viruses. We received the well-characterized challenge material (WCCM) from BEI Resources (Manassas, VA), which includes isolates of SARS-CoV-2 [NR-55612: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/PHC658/2021 (Lineage B.1.617.2; Delta Variant), NR-58620: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/COR-22-063113/2022 (Lineage BA.5; Omicron Variant)], NR-56462: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/MD-HP20874/2021 (Lineage B.1.1.529; Omicron Variant) and SARS-CoV (NR-15418 SARS coronavirus Urbani v2163). We amplified the viruses in Vero E6 cells to create working stocks of the virus. The virus was adapted to mice by four serial passages in the lungs of mice and plaque purified at Utah State University (USU).

Biosafety and Ethics. The animal experiments at USU were conducted in accordance with an approved protocol by the Institutional Animal Care and Use Committee of USU. The work was performed in the AAALAC-accredited LARC of the university in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals (8th edition; 2011).
Viral challenge studies in animals

Animals: For SARS-CoV-2 animal studies completed at USU, 6–10-week-old male and female golden Syrian hamsters (Mesocricetus auratus) were purchased from Charles River Laboratories (Strain code: 049) and housed in the ABSL-3 animal space within the LARC. All hamsters included in the study were carefully matched for age. The hamsters were not bred on-site. All hamsters were singly housed while at the facility.

Infection of animals. Hamsters were anesthetized with isoflurane and infected by intranasal instillation of 1 × 104.5 CCID50 (cell culture infectious dose 50%) of SARS-CoV-2 in a 100 µl volume.

Titration of tissue samples: Lung tissue and nasal tissue samples from hamsters were homogenized using a bead-mill homogenizer using minimum essential media. Homogenized tissue samples were serially diluted in a test medium, and the virus was quantified using an endpoint dilution assay on Vero E6 cells for SARS-CoV-2. A 50% cell culture infectious dose was determined using the Reed-Muench equation72.
Transmission studies

We immunized hamsters with a dual dose of the intranasal NanoSTING-SN vaccine or PBS, 5 weeks (day-21) and 2 weeks (Day 0) prior to infection with ∼3 × 104 CCID50 of SARS-CoV-2 Omicron VOC (BA.5) [day 14]. One day after the viral challenge, we co-housed the index hamsters in pairs with contact hamsters for 4 days in clean cages. We euthanized the index and contact hamsters on day 4 and day 5 of cohousing. Viral titers in the lungs and nasal tissue of the index and contact hamsters were used as primary endpoints. We performed another study with another strain of SARS-CoV-2 Omicron VOC (B.1.1.529). We immunized hamsters with a single dose of the intranasal NanoSTING-SN vaccine or PBS, 3 weeks prior to infection with ∼3 × 104 CCID50 of SARS-CoV-2 Omicron VOC (B.1.1.529). One day after the viral challenge, we co-housed the index hamsters in pairs with contact hamsters for 4 days in clean cages. We euthanized the contact and index hamsters on day 4 of cohousing. Viral titers in the nasal tissue of the index and contact hamsters were used as primary endpoints.
Histopathology

Lungs of the Syrian golden hamsters were fixed in 10% neural buffered formalin overnight and then processed for paraffin embedding. The 4-μm sections were stained with hematoxylin and eosin for histopathological examinations. We used integrated scoring rubric for evaluating the pathology score73. The scoring method in the reference was modified from a 0–3 to a 0–4 score with 1 = 1–25%, 2 = 26–50%; 3 = 51–75; 4 = 76–100%, so with the three criteria mentioned in the reference will yield a score for an animal ranging from 0–12. This scoring also takes into account the degeneration/necrosis of the bronchial epithelium/alveolar epithelium. A board-certified pathologist evaluated the sections.
Quantitative modeling

To quantify the kinetics of SARS-CoV-2 infection in the upper respiratory tract (URT) upon N, S, and N + S immunization, we modified a previously described innate immune model46. We added appropriate parameters to account for de-novo blocking and T-cell killing, as shown in Fig. 2A. The mean population parameter values and initial values were from prior publication46. We solved the system of ordinary differential equations (ODEs) for different S and N response efficiencies using the ODE45 function in MATLAB 2018b. A sample MATLAB code for solving the system of equations has been provided in Sup Note 1. There are some limitations to our model. This model does not consider the effect of interferons that are known to suppress viral production rate. Under these conditions, the rate constant π, for viral production should reduce as the infection progresses and this factor is especially important when the infection persists >7 days46. Second, our model in Supplementary Fig. 5C predicts that the number of viral particles is between 1 and 100 which is below the experimental detection limit and hence cannot be confirmed experimentally.
Immunogenicity studies in rhesus macaques (RM’s) and their monitoring

Experiments with rhesus macaques (M. mulatta) were reviewed and approved by UH IACUC. Three healthy rhesus macaques (RM’s) of Indian origin, between 4 and 11 years of age and 4–12 kg in weight) were used. The RM’s were acquired from Washington University School of Medicine, Division of Comparative Medicine C/O Dr. Chad B Faulkner; 660S. Euclid Ave., Box 8061; St. Louis, MO 63110 and Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop, TX. We used three RM’s for the study. Two of them were males, and one was female. All the animals were single-housed. We administered two doses of the intranasal NanoSTING-SN vaccine (n = 3/group), 28 days apart to RM’s The animals were monitored until day 44 for changes in body weight, attitude, appetite, body temperature (via a rectal thermometer). For evaluating humoral immune responses, we collected the sera and nasal washes on day 0, 7, 14, 28, and 44. We kept the blood at 25 °C for 10 min to facilitate clotting and centrifuged it for 5 min at 2000 × g. We collected the sera, stored it at −80 °C, and used it for ELISA. We kept the sera and nasal wash fluid [with protease inhibitors (Roche, #11836153001] at −80 °C for long-term storage.
NHP ELISA

For NHP serum IgG and IgA ELISA, we coated the plate overnight with 0.5 μg/ml S protein and 1 μg/ml N protein (Acrobiosystems, DE, USA). The MERS spike protein (BEI resources, VA, USA) was also coated at 0.5 μg/ml. Subsequent blocking and wash steps were performed similarly to the mouse IgG and IgA ELISAs. Serum and nasal wash samples from NHPs were added at different dilutions and incubated for 1 h at room temperature. Mouse anti-monkey IgG HRP (Southern Biotech, 1: 5000; AL, USA) was used to detect IgG in serum and nasal wash samples. IgA was detected using goat anti-monkey IgA HRP from Exalpha (MA, UK) at 1:5000 dilution. Pre-immunization sera was used as control for ELISA. The threshold for positivity was set at an optical density (450 nm) value of 0.05 or two times the negative control (PBS), whichever was higher. Endpoint titers were defined as the lowest dilution that was higher than the threshold for positivity.
NHP RBD ELISA

We evaluated RBD-specific serum IgG and IgA in NHPs using indirect ELISAs. We coated the plates with 0.5 μg/ml spike RBD proteins (BA.1 variant: Cat# NR- SPD-C522j, ACROBiosystems, DE, USA); (XBB1.5 variant: Cat# SPD-C5242, ACROBiosystems, DE, USA). We incubated the plates overnight at 4 °C or 2 h at 37 °C. The unbound protein was washed off by rinsing the wells twice with PBS + 0.05% Tween-20 (PBST). The remaining active protein binding sites on the plates were blocked off by incubating the plates with PBS + 1% BSA + 0.1% Tween-20 for 1 h at room temperature. After two additional washes with PBST, we added the serum samples serially diluted in PBST + 0.5% BSA. Endpoint titers were evaluated by adding serum samples in two-fold dilutions in duplicates. Following 1 h of incubation at RT with diluted serum, we washed the plates four times with PBST and added HRP-conjugated anti-human IgG (Cat# 6200-05, Southern Biotech, 1: 80000); AL, USA to detect RBD protein-specific IgG. For the detection of IgA in serum, we used mouse anti-monkey IgA biotin (Cat# MCA2553B, BioRad, 1: 10000; CA, USA). We incubated the plates with detection antibodies for 1 h at room temperature. We washed the plates four times with PBST and added Streptavidin-HRP (Vector Laboratories, 1: 5000, CA, USA) to detect the anti-IgA biotin antibodies. Finally, we washed the plates four times with PBST before adding 100 μl 1-Step™ TMB ELISA Substrate Solution (Cat# 34021, ThermoFisher, MA, USA). The plates were incubated with TMB for 30 min at RT, and we added 2 M H2SO4 to stop color development. We recorded optical density (OD) values using Cytation 7 (Biotek Instruments Inc).
Statistics and reproducibility

Statistical significance was assigned when P values were <0.05 using GraphPad Prism (v6.07). Tests, number of animals (n), mean values, statistical comparison groups, and the statistical test used are indicated in the figure legends. No statistical methods were used to predetermine sample sizes for the in-vitro and animal studies. Sample size was determined based on similar studies in this field. Animals were randomly divided into experimental groups. When applicable, technical repeats are specified for each experiment in the figure legends wherever applicable. No data was excluded from the analyses. Animal studies were performed in biological triplicates or more, as indicated in the figure legends. Reproducibility between animals in NanoSTING, NanoSTING-N, and NanoSTING-SN and PBS groups is shown in the results and figure legends. The researchers were not blinded to allocation during experiments and outcome assessment. Data collection and analysis were not performed blind to the conditions of the experiments. The pathologists performing the histopathological analysis were blinded to treatment. The adjuvant was manufactured at UH, and the adjuvant/protein were shipped to USU. USU performed the vaccine formulation for the challenge experiments and immunized and challenged the animals. Further information on research design is available in the Nature Research Reporting Summary linked to this article.
Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.
Data availability

All data are included in the source data file or available from the authors, as are unique reagents used in this article. The raw numbers for charts and graphs are available in the Source Data file whenever possible. All material and experimental data requests should be directed to the corresponding author, Navin Varadarajan. Source data are provided with this paper.
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Acknowledgements

This publication was supported by the NIH (R01GM143243), AuraVax Therapeutics, and Owens Foundation. X.L. acknowledges partial funding support from the National Cancer Institute (NIH R15CA182769, P20CA221731, P20CA221696) and CPRIT (RP150656). The following reagents were produced under HHN272201400008C and obtained through BEI Resources, NIAID, NIH: Spike Glycoprotein (Stabilized) from SARS-Related Coronavirus 2, Wuhan-Hu-1, Recombinant from Baculovirus, NR-52308; and Spike Glycoprotein Receptor Binding Domain (RBD) from SARS Related Coronavirus 2 (multiple variants), NR-55612: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/PHC658/2021 (Lineage B.1.617.2; Delta Variant): This reagent was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/USA/PHC658/2021 (Lineage B.1.617.2; Delta Variant) (WCCM), NR-55612, contributed by Dr. Richard Webby and Dr. Anami Patel. NR-58620: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/COR-22-063113/2022 Lineage BA.5; Omicron Variant: This reagent was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/USA/COR-22-063113/2022 (Lineage BA.5; Omicron Variant) in VeroTMPRSS2-ACE2 Cells (WCCM), NR-58620, contributed by Dr. Richard J. Webby. NR-56462: SARS-Related Coronavirus 2 Isolate hCoV-19/USA/MD-HP20874/2021 (Lineage B.1.1.529; Omicron Variant) was obtained through BEI Resources, NIAID, NIH: SARS-Related Coronavirus 2, Isolate hCoV-19/USA/MDHP20874/2021 (Lineage B.1.1.529; Omicron Variant) (WCCM), NR-56462, contributed by Andrew S. Pekosz. NR-15418: SARS coronavirus Urbani v2163: Severe acute respiratory syndrome coronavirus (SARS-CoV), strain Urbani (200300592), was obtained from the Centers for Disease Control and Prevention (CDC, Atlanta, GA) and routinely passaged in Vero-76 cells. This virus was adapted through 25 serial passages in the lungs of mice and plaque-purified for use in mouse infections74. Schematics were made using Adobe Illustrator, Microsoft PowerPoint, and Biorender via full license.
Author information
Author notes

    These authors contributed equally: Ankita Leekha, Arash Saeedi.

Authors and Affiliations

    William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA

    Ankita Leekha, Arash Saeedi, K M Samiur Rahman Sefat, Monish Kumar, Melisa Martinez-Paniagua, Adrian Damian, Rohan Kulkarni, Kate Reichel, Ali Rezvan & Navin Varadarajan

    Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA

    Shalaleh Masoumi & Xinli Liu

    AuraVax Therapeutics, Houston, TX, USA

    Laurence J. N. Cooper & Manu Sebastian

    Animal Care Operations, University of Houston, Houston, TX, USA

    Courtney M. Sands

    College of Optometry, University of Houston, Houston, TX, USA

    Vallabh E. Das & Nimesh B. Patel

    Institute of Antiviral Research, Utah State University, UT, Logan, USA

    Brett Hurst

Contributions

N.V. conceived the study. N.V., A.L., A.S., L.J.N.C., M.S., and B.H. designed the study. A.L., A.S., K.M.S.R.S., M.K., M.M.P., A.D., R.K., K.R., A.R., S.M., B.H., C.M.S., V.E.D., M.S., N.B.P., and X.L. performed experiments. A.L., A.S., K.M.S.R.S., M.K., B.H., X.L., and N.V. analyzed the data. M.K. performed modeling. N.V., A.L. drafted the manuscript, and all authors contributed to the review and editing of the manuscript.
Corresponding author

Correspondence to Navin Varadarajan.
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Competing interests

UH has filed a provisional patent based on the findings of this study. N.V. and L.J.N.C. are co-founders of AuraVax Therapeutics and CellChorus. The remaining authors declare no competing interests.
Ethical approval

The mouse, hamster, and NHP studies were performed under the study protocol (PROTO2020000019, PROTO202100006, PROTO202100049, PROTO202200025), as approved by the Institutional Animal Care and Use Committee in University of Houston. The animal experiments at USU were conducted in accordance with an approved protocol by the Institutional Animal Care and Use Committee of Utah State University. The work was performed in the AAALAC-accredited LARC of the university in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals (8th edition; 2011).
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Nature Communications thanks Juliane Schröter, Yi-Nan Zhang, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. A peer review file is available.
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Leekha, A., Saeedi, A., Sefat, K.M.S.R. et al. Multi-antigen intranasal vaccine protects against challenge with sarbecoviruses and prevents transmission in hamsters. Nat Commun 15, 6193 (2024). https://doi.org/10.1038/s41467-024-50133-2

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    Received01 August 2023

    Accepted01 July 2024

    Published23 July 2024

    DOIhttps://doi.org/10.1038/s41467-024-50133-2

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    Mucosal immunology
    Protein vaccines
    SARS-CoV-2
    Viral infection

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