Shielding Replicating Single-cycle Vaccines against SARS-CoV-2

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Abstract Many COVID-19 vaccines are replication-defective mRNA, DNA, or adenovirus (Ad) vaccines. In each case, the vaccine delivers its one copy of an antigen gene and expresses "1X" of the antigens that are encoded by the vaccine. We developed single cycle Ad (SC-Ad) vaccines that replicate vaccine antigen genes up to 10,000-fold in every cell to amplify antigen production but do not produce infectious progeny viruses. When RD-Ad and SC- Ad6 expressing SARS-CoV-2 are compared, SC-Ad produces 100 times more spike protein than RD-Ad and significantly higher spike antibodies than RD-Ad-Spike. When the animals were challenged 10.5 months after single immunization, SC-Ad reduced SARS-CoV-2 lung viral loads and damage and preserved body weights better than RD-Ad. However, observations of vaccine-induced thrombotic thrombocytopenia (VITT) in Ad26 and ChAdOx-1 COVID-19 vaccine trials endanger the prospects of SC-Ad and all other adenovirus vaccines. In one hypothesis, VITT is thought to be caused by the binding of PF4 to the hexons of Ad26 and ChAdOx-1. This complex is thought to provoke antibodies against PF4 that cause VITT. While VITT could theoretically occur with any adenovirus, the particular serotype of each Ad may influence the risk of this side effect. Different Ad serotypes vary in the hypervariable regions (HVRs) of their hexon proteins. These HVRs determine whether the antibodies and other proteins like PF4 bind or do not bind each adenovirus. We hypothesize that the natural binding of blood proteins to species C Ads may naturally shield them from PF4 binding whereas other serotypes are at risk of PF4 binding. One can also genetically and chemically engineer Ads to proactively shield them from interactions with antibodies and PF4. We hypothesize that genetic and chemical shielding can be used to make safer SC-Ad and other Ads for vaccination against SARS-CoV-2 and other pathogens. This project will test these hypotheses in three Specific Aims. In the first, we will perform high resolution cryo- electron microscopy to examine the interactions of PF4 and other proteins on species C and species D adenoviruses. In the second aim, we will compare the utility of genetic and chemical shielding strategies to protect Ads from PF4 and also against neutralizing antibodies. In the third aim, we will test if different Ad serotypes bound to PF4 can provoke VITT in animal models, whether this is different for different serotypes, and whether genetic and chemical shielding can maintain vaccine efficacy while mitigating the risks of VITT induction. Successful pursuit of this project will lead to better understanding of natural binding of blood clotting factors to different serotypes and how this affects their in vivo biology and side effects. This project will also test and optimize proactive strategy to increase adenovirus vaccine safety for SARS-CoV-2 and future pathogen targets. This can have utility for vaccines, gene therapy, or oncolytic adenoviruses to increase efficacy and safety and protect them from not only PF4, but also against problematic vector neutralizing antibodies.