Rational design and development of an interferon-integrated universal sarbecovirus vaccine

Abstract

The development of the pan-sabecovirus vaccine has become an urgent need in response to the threats caused by sarbecoviruses and future pandemics. Here, we designed a platform to generate an intranasal live-attenuated vaccine to elicit a broad immune response against sabecovirus. The vaccines generated by this platform was attenuated by the defective envelope gene and the replacement of orf8 segment with interferon-beta expression cassette. Therefore, this vaccine platform was named as Interferon-Beta-Integrated SARS-CoV-2 (IBIS) vaccine platform. Two generations of vaccines, IBIS-1 and IBIS-2, were included in this platform. The first-generation IBIS, IBIS-1, utilized SARS-CoV-2 ancestral strain as the backbone of the vaccine. Mouse interferon-beta (IFNβ) expression cassette replaced the orf8 segment of the virus for the animal trials. The in vitro data proved that IBIS-1 was safe and exhibited single round infection. The replication ability of IBIS-1 only restored in the presence of envelope proteins. In addition, the mouse IFNβ was expressed successfully by the virus. Building on the success of IBIS-1, we progressed it to the second-generation IBIS, IBIS-2, for human application by utilizing human IFNβ instead of mouse IFNβ. During the preparation and modification of IBIS-2, the orf6, orf7a, orf7b and orf8 segments were removed to increase its genome stability. Furthermore, to prepare for future clinical trials and to further optimize the safety profile of the vaccine, Omicron variant was utilized as the backbone of IBIS-2. This strategic modification aims to reduce the potential for genetic recombination and enhance the immunogenicity of the vaccine. Two versions were included in IBIS-2: envelope-defective (IBIS-2SR) and envelope-competent (IBIS-2MR). Both versions showed similar replication properties and replication kinetics. They showed single round infection in the cells, which had competent IFN signalling, and restored the multiple round infection in defective IFN signalling and envelope-expressing cells. Functional human IFNβ was produced successfully by both IBIS-2. Both versions were tested on hamsters and protected the hamsters from SARS-CoV-2 infection. No viral load was detected in the lung and nasal turbinates of the hamsters after infection. Furthermore, no histopathological changes in lung of the vaccinated hamsters or pro-inflammatory cytokine induction in the lung tissues after infection, which affirmed the safety and efficacy of both IBIS-2. In addition, the attenuation of IBIS provided an insight to generate a safe and live reporter virus for drug screening and neutralisation assay, which are usually performed in BSL-3 laboratory when handling authentic virus. A live-attenuated virus with the integration of nano-luciferase expression cassette integrated into the virus, named as NLucIS, was generated and utilized in drug screening system and neutralisation assay. It showcased the platform’s potential for board application beyond vaccination. IBIS platform is a potential next-generation solution for sarbecovirus outbreaks. The platform shows a promising safety profile that supports its advancement into human clinical trials. The IBIS platform represents a significant advancement in our preparedness for future pandemics caused by SARS-like coronaviruses as the vaccines are able to elicit a strong and broad immune response with minimized safety risks.