Development of Intranasal SARS-CoV-2 vaccines based on the influenza virus-vector

Abstract

Immunization has been crucial in mitigating the burden of COVID-19 since the introduction of SARS-CoV-2 vaccines in late 2020. However, the emergence of viral variants has impacted the efficacy of current vaccines, as these variants exhibit significant immune evasion. Additionally, existing vaccines are limited in their ability to induce long-lasting sterilizing immunity or local mucosal immunity in the respiratory tract, which are vital for preventing SARS-CoV-2 transmission. There is a pressing need for next-generation vaccines that offer improved protection by preventing infections altogether. In this thesis, a novel intranasally administered influenza virus-vectored SARS-CoV-2 vaccine candidate called DelNS1-RBD4N-DAF was developed and evaluated in animal models. This vaccine is a live attenuated influenza virus modified through deletion of the NS1 gene that expresses the receptor binding domain (RBD) of a selected SARS-CoV-2 spike protein. To improve immunogenicity, the vaccine incorporated modifications to the RBD antigen, namely targeting for N-linked glycosylation and fusion to decay accelerating factor (DAF), a membrane-anchored protein peptide. The efficacy of the DelNS1-RBD4N-DAF vaccine was assessed in BALB/c mice and Syrian hamsters. Following intranasal two doses of prime-boost vaccination, the DelNS1-RBD4N-DAF vaccine induced robust levels of neutralizing antibodies against different SARS-CoV-2 variants, including Delta, Omicron BA.1, and Omicron BA.2, in the serum of mice and hamsters. Additionally, strong T cell responses were elicited in mice. Notably, the DelNS1-RBD4N-DAF vaccine offered superior cross-protection against SARS-CoV-2 variant challenges in both the upper and lower respiratory tracts of mice and hamsters when compared to the intramuscular BNT162b2 mRNA vaccine. Importantly, the DelNS1-RBD4N-DAF vaccine also provided protection against influenza virus infection in mice. The rapid evolution of SARS-CoV-2 has diminished the usefulness of existing vaccines due to immune evasion mutations primarily found in the spike protein of new variants. Exploring non-spike epitopes as vaccine targets is an alternative strategy that may provide broader protection against emerging SARS-CoV-2 variants or potentially even emerging novel coronaviruses. My study focused on evaluation of the nucleocapsid protein (NP) of SARS-CoV-2 as a potential vaccine antigen candidate using the DelNS1 influenza virus vector platform. Mice and hamsters intranasally immunized with NP-based vaccines were observed to mount both cellular and humoral immune responses. The T cell response was found to play a critical role in providing protection against SARS-CoV-2 infection. These findings provide insights into the potential of NP antigens for developing next-generation vaccines against SARS-CoV-2. In conclusion, I have developed and evaluated SARS-CoV-2 vaccines using the DelNS1 influenza virus vector vaccine platform, targeting the receptor binding domain (RBD) of the spike protein and also the nucleocapsid protein (NP). These vaccines induced significant protection against both SARS-CoV-2 and influenza virus infection in animal models. The influenza-based viral vector platform has the potential to be utilized for the development of bivalent vaccines against both influenza and COVID-19 or other respiratory virus infections, including future emerging viruses.