Countermeasures against COVID-19

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1. Intranasal single-dose vaccination with VSV-based COVID-19 vaccines protects rodents from disease We designed, cloned, and recovered two replication-competent VSV-based vaccines encoding the SARS-CoV-2 spike protein either alone (VSV-SARS2) or in combination with the EBOV GP (VSV-SARS2-EBOV). EBOV GP was included to enable ACE2-independent vaccine replication in the host and to possibly expand target cell tropism. We vaccinated hamsters by the intranasal (IN) or intramuscular (IM) routes 28 days prior to challenge with four SARS-CoV-2 VOC: the ancestral, alpha, beta, and delta variants. IN vaccination with either the VSV-SARS2 or VSV-SARS2-EBOV resulted in the highest protective efficacy, as demonstrated by decreased virus shedding and lung viral load in vaccinated hamsters. Histopathologic analysis of the lungs revealed the least amount of lung damage in the IN-vaccinated animals regardless of the challenge virus. In addition, IN-vaccination resulted in protection within 10 days and the animals did not show any clinical or significant histopathologic signs of COVID-19 pneumonia when challenged with the ancestral SARS-CoV-2 strain or the alpha or beta variants (ODonnell et al., Frontiers in Immunology 2021; ODonnell et al., Vaccines 2022). In FY23, we showed that a VSV-based vaccine expressing the SARS-CoV-2 S plus the conserved nucleocapsid (N) protein was protective in a hamster challenge model when a single dose was administered 28 or 10 days prior to challenge, respectively. In this study, only IN vaccination resulted in protection against challenge with multiple VOC highlighting that the addition of the N protein indeed improved protective efficacy. This data demonstrates the ability of a VSV-based dual-antigen vaccine to reduce viral shedding and protect from disease caused by SARS-CoV-2 VOC (ODonnell et al. Front Immunol 2022). Furthermore, we conducted an over 12-month long vaccine durability study in mice. The study has been completed, data analysis is ongoing and revealed that vaccine-mediated protection wanes around 6-9 months after vaccination with total IgG and neutralizing antibody titers decreasing. Studies investigating the cellular response are ongoing (ODonnell et al. manuscript in preparation). Ongoing studies also investigate early immune responses after vaccination in the mouse model with the aim to decipher mechanisms contributing to the fast onset of protection (Anhalt et al., unpublished data). 2. VSV-SARS2-EBOV protected NHPs within 10 days when administered IM but not IN We vaccinated NHPs with a single dose of 107 PFU of the vaccine by the IM or IN route, while NHPs vaccinated IN or IM with 107 PFU VSV-EBOV served as controls. Challenge with SARS-CoV-2 WA1 by multiple routes as described previously occurred 10 days later. At 7 days after challenge, all NHPs were euthanized for sample collection. NHPs IM-vaccinated with VSV-SARS2-EBOV were protected within 10 days and did not show signs of COVID-19 pneumonia. In contrast, IN vaccination resulted in limited immunogenicity and enhanced COVID-19 pneumonia compared to controls. The IN-vaccinated NHPs exhibited lung lesions and presented with more lung infiltrates compared to the IM and control groups at the time of euthanasia (Furuyama et al., mBio 2022). 3. SARS-CoV-2 VOC infection induces similar disease but distinct humoral responses and transcriptomic changes in Syrian golden hamsters Following the discovery of SARS-CoV-2 and its rapid spread throughout the world, new viral variants of concern (VOC) have emerged. There is a critical need to understand the impact of the emerging variants on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Syrian golden hamsters are the leading small animal model that recapitulates key aspects of severe COVID-19. We performed intranasal inoculation of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1-2020) or VOC first identified in the United Kingdom (B.1.1.7, alpha) and South Africa (B.1.351, beta) and analyzed viral loads and host responses. Similar gross and histopathologic pulmonary lesions were observed after infection with all three variants. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of challenged animals, infectious titers in the lungs were comparable between the variants. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Transcriptional profiling of lung samples 4 days post-challenge (DPC) was performed in collaboration with Dr. Ilehm Messaoudi and indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.1.7 infection. Furthermore, no additional mutations in the spike protein were detected at 4 DPC. Although disease severity and viral shedding were not significantly different, the emerging VOC induced distinct humoral responses and transcriptional profiles compared to the ancestral virus. These observations suggest potential differences in acute early responses or alterations in immune modulation by VOC (ODonnell et al., eBioMedicine 2021). 4. Analysis of human COVID-19 serum samples In order to expand our understanding of human cytokine responses during COVID-19, we analyzed human serum samples collected over time from patients from Indiana (collaboration with Dr. Ryan Relich). SARS-CoV-2 infection results in a variety of clinical symptoms ranging from no or mild to severe disease. We examined serum and plasma from a cohort of patients infected with SARS-CoV-2 early in the pandemic and compared them to negative-control sera. Cytokine and chemokine concentrations varied depending on the severity of infection, and antibody responses were significantly increased in severe cases compared to mild to moderate infections. Neutralization data revealed that patients with high titers against an early 2020 isolate had detectable but limited neutralizing antibodies against the emerging SARS-CoV-2 Alpha, Beta and Delta variants. This study highlights the potential of re-infection for recovered COVID-19 patients (Griffin et al., Sci Rep 2021). In FY22, we also supported a study by Prof. Ayato Takada (Hokkaido University, Japan) exploring the potential risks of antibody-dependent enhancement (ADE) in COVID-19. Clinical importance of ADE is unclear since the proposed ADE mechanism mostly depends on the Fc receptor (FcR) expressed exclusively on immune cells which are not primary targets of SARS-CoV-2. We show that SARS-CoV-2 utilizes at least two distinct ADE mechanisms, FcR-mediated and FcR-independent complement component C1q-mediated pathways. We found that both FcR- and C1q-mediated ADE activities were detectable in the sera of acute and convalescent COVID-19 patients at a high rate. Although neutralizing activity was also detected, it was counteracted by ADE at subneutralizing conditions in the presence of FcR or C1q. Considering the ubiquity of C1q and its cellular receptors, our data suggest that C1q-mediated ADE may more likely occur in respiratory epithelial cells, which SARS-CoV-2 primarily infects (Okuya et al., Microbiology Spectrum 2022). 5. Protection from COVID-19 by nanobodies In FY23, we conducted collaborative studies on the development of SARS-CoV-2-specific nanobodies in collaboration with Dr. Charles K.F. Chan at Stanford university. He is exploring nanobodies as a therapeutic approach against respiratory diseases and COVID-19 was used as a proof-of-concept virus. Intranasal or aerosol administration of the nanobody before intranasal SARS-CoV-2 infection protected the majority of hamsters from severe disease (ODonnell et al. unpublished data). This approach is currently under investigation for respiratory syncytial virus.