Countermeasures against COVID-19

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Summary 1. Intranasal single-dose vaccination with VSV-based COVID-19 vaccines protects hamsters from disease within 10 days 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. Growth kinetics in cell culture confirmed superior replication of the VSV-SARS2-EBOV vaccine in VeroE6 cells. Using the well-established Syrian golden hamster model of COVID-19, we compared vaccine immunogenicity after a single intranasal (IN) or intramuscular (IM) dose of 105 PFU. IN vaccination resulted in an early CD8+ T cell response in the lungs and a greater total antigen-specific IgG response by ELISA compared to IM-vaccinated and control hamsters. In addition, the neutralizing response was also increased after IN vaccination compared to IM. In contrast, IM-vaccinated hamsters developed an early CD4+ T cell response. For the protective efficacy study, we vaccinated hamsters IN or IM 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. These data demonstrate the ability of VSV-based vaccines to not only protect from disease caused by SARS-CoV-2 VOC, but also to reduce viral shedding (ODonnell et al., Frontiers in Immunology 2021; ODonnell et al., Vaccines 2022). 2. VSV-SARS2-EBOV protected NHPs within 10 days when administered IM but not IN This project investigated the protective efficacy of a single dose of the VSV-SARS2-EBOV vaccine in rhesus macaques based on the superior performance of this vaccine after IM administration -the approved route for VSV-EBOV vaccination in humans - in hamsters as demonstrated above. 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. Histological examination of the lung tissue revealed immunopathology that was most significant in IN-vaccinated animals. Importantly, IM-vaccinated animals did not develop signs of interstitial pneumonia, nor could we detect SARS-CoV-2 antigen in the lungs. Indeed, at the time of euthanasia, lung lesions were apparent in animals from the IN and control groups, but not in the IM group (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 There was a critical need to understand the impact of the emerging SARS-CoV-2 VOC on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Syrian golden hamsters are the leading small animal model recapitulating key aspects of severe COVID-19. In this project, we demonstrated that IN inoculation of 105 TCID50 of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1-2020) or VOC first identified in the United Kingdom (alpha, B.1.1.7) and South Africa (beta, B.1.351) led to similar gross and histopathologic pulmonary lesions 4 days after challenge. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of infected hamsters, infectious titers in the lungs were comparable. At 14 days after challenge, lung pathology was mostly resolved for all challenged hamsters in this non-lethal model. While there was no difference in the S-specific IgG titers at either 14 or 28 days after challenge among the groups, IgG specific to the S receptor-binding domain (RBD) was significantly increased in hamsters infected with B.1.351 compared to B.1.1.7. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Bulk RNA sequencing of lung samples collected 4 days after challenge was performed. Principal component analysis revealed distinct separation between uninfected and infected hamsters, with the B.1.1.7 infection resulting in the most distinct transcriptional profile and the largest number of differentially expressed genes (DEGs)(n=1,277) while infection with B.1.351 resulted in the smallest number of DEGs (n=395). Transcriptional profiling indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.351 infection. Furthermore, no additional mutations in the spike protein were detected at peak disease. These observations document differences in acute early responses or alterations in immune modulation by VOC potentially impacting the efficacy of existing vaccines and therapeutics. 4. Analysis of human COVID-19 serum samples reveals 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. SRAS-CoV-2 infection results in a variety of clinical symptoms ranging from no or mild to severe disease. Currently, there are multiple postulated mechanisms that may push a moderate to severe disease into a critical state. Human serum contains abundant evidence of the immune status following infection. Cytokines, chemokines, and antibodies can be assayed to determine the extent to which a patient responded to a pathogen. 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). 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 (Okuya et al., Microbiology Spectrum 2022).