Rational design of a unique vaccine for emerging pandemic coronaviruses

Abstract SARS-CoV-2 has caused the global COVID-19 pandemic. Vaccines against SARS-CoV-2, mostly using spike (S) protein as a target antigen to induce neutralizing antibodies, have been developed at unprecedented speed and several have been approved for use in human. The currently developed vaccines induce neutralizing antibodies and provide protection against SARS-CoV-2 original strain or earlier variants, but they have reduced neutralizing activity or protection against recent variants. Based on the fact that three pandemic coronaviruses (CoVs) have emerged within 20 years, some unknown CoVs with pandemic potential are expected to emerge in the foreseeable future. Therefore, a vaccine is urgently needed to prevent a future emerging CoV. Three CoV outbreaks caused by the three highly pathogenic CoVs (SARS-CoV, SARS-CoV-2 and MERS-CoV) are all from beta-CoVs, in particular, from Sarbecovirus and Merbecovirus lineages, we thus reason that future emerging CoVs causing pandemics may most likely come from these two lineages and that both lineages should be targeted to develop a vaccine to prevent against the future emerging virus. However, we cannot predict the sequences of S protein of future emerging CoV to make a vaccine targeting S to induce neutralizing antibodies. Our prior data showed that a S protein-based vaccine by using ubiquitination and gene rearrangement strategy to enhance its degradation in proteasome induced strong T cell responses, in particular CTLs. This vaccine significantly protected mice against SARS-CoV-2-induced survival and weight loss, and the protection required CD4+ and CD8+ T cells. Thus, we will design CoV vaccines that target the proteins with great homology (i.e., S2, M, and N) from Sarbecoviruses and Merbecoviruses to induce protective T cells. Furthermore, upper respiratory tract tissue-resident memory T cells (TRM) play essential roles in providing immediate protection, and mucosal immunization is the only way to induce upper respiratory tract TRM. Because papillomavirus-like particles (PV- VLPs) induce mucosal immune responses, which serve as a mucosal delivery vector and adjuvant, we hypothesize that PV-VLPs can deliver CoV homologous antigens to nasal-associated lymphoid tissue, and induce respiratory tract TRM for effective protection against Sarbecovirus and Merbecovirus-caused respiratory syndrome and pneumonia. Using Sarbecoviruses and Merbecoviruses as model viruses, this proposal will 1) develop a PV-VLP-based, T cell-inducing mucosal CoV vaccine targeting conserved CoV antigens (S2, M and N) and using gene rearrangement and ubiquitination strategies, 2) determine if the vaccine induces mucosal and systemic immune responses to Sarbecoviruses and Merbecoviruses, in particular, long-term upper respiratory tract TRM, and 3) evaluate vaccine's cross-protective efficacy against infections of Sarbecoviruses and Merbecoviruses in mouse models. We have solid preliminary data, well-established animal models and vaccine platforms, and a strong research team with decades of extensive experience in developing safe and effective CoV vaccines, providing feasibility and basis for the proposed studies.