Receptor recognition of SARS-CoV-2 and vaccine design

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Receptor recognition of SARS-CoV-2 and vaccine design

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SARS-CoV-2, the causative agent of COVID-19, has devastated the world with many waves of variants of concern (VOC) over these two years. The current highly contagious and fast-spreading omicron variants of SARS-CoV-2 infect the respiratory tracts efficiently. The receptor-binding domain (RBD) of the omicron spike protein recognizes human ACE2 as its receptor and plays a critical role in the tissue tropism of SARS-CoV-2. Here, we showed that the omicron RBD binds to ACE2 more strongly than does the prototypic RBD from the original Wuhan strain. We also measured how individual omicron mutations affect ACE2 binding. We further determined the crystal structure of the RBD complexed with ACE2 at 2.6 Å. The structure shows that omicron mutations caused significant structural rearrangement of two mutational hotspots at the RBD/ACE2 interface, elucidating how each omicron mutation affects ACE2 binding. The enhanced ACE2 binding by the omicron RBD can facilitate the omicron variant to infect the respiratory tracts where the ACE2 expression level is low. Our study provides insights into the receptor recognition and tissue tropism of the omicron variant. Besides the SARS-CoV-2 omicron variant, other VOCs, such as alpha, beta, gamma, and delta variants, are also associated with increased transmissibility and virulence, and the possible emergence of escape mutations. Studies have indicated that intermediate horseshoe bats and pangolins are potential reservoirs of SARS-CoV-2. Furthermore, recent evidence also shows that SARS-CoV-2 is able to jump between humans and minks, which raises concerns about the prevention and control of SARS-CoV-2, as the spillover of SARS-CoV-2 is associated with potential mutations. Here we measure the binding affinities of SARS-CoV-2 VOC RBDs to human mink, pangolin, or intermediate horseshoe bat ACE2s by surface plasmon resonance (SPR) assay, and find that SARS-CoV-2 VOC RBDs can bind to mink, pangolin, and intermediate horseshoe bat ACE2s with a differential level of affinities, albeit human ACE2 has the highest binding affinities. To elucidate the detailed interaction mechanisms, besides the crystal structure of the Omicron (BA.1) RBD with human ACE2, the crystal structures of the complexes of SARS-CoV-2 VOC-specific RBD with human ACE2, and SARS-CoV-2 RBD with pangolin and mink ACE2s are determined at 2.61 Å, 2.98 Å, and 2.76 Å, respectively. These structures adopt similar binding patterns with two hotspot bind sites in the RBD/ACE2 interface. The residue variations of the two hotspots in the RBD/ACE2 interface are mainly responsible for the differential binding affinities of SARS-CoV-2 variant RBDs to human ACE2, and SARS-CoV-2 RBD to pangolin and mink ACE2s. We further measure the binding affinities and provide structural analysis of the species-specific SARS-CoV-2 RBD mutations to the binding of cross-species ACE2s by SPR. Overall, this study provides more structural evidence of the interaction of SARS-CoV-2 variant RBDs with human ACE2, and cross-recognition of SARS-CoV-2 RBD to pangolin and mink ACE2s. The facts that SARS-CoV-2 VOCs can bind to other species’ ACE2s, and species-specific SARS-CoV-2 RBD mutations differentially impact cross-species ACE2s’ binding affinities, highlight the need for surveillance of the viral genome from infected animals and humans, particularly the genome regions affecting diagnostic tests, antiviral therapies, and vaccine development.The key to battling the COVID-19 pandemic and its potential aftermath is to develop a variety of vaccines that are efficacious and safe, elicit lasting immunity, and cover a range of SARS-CoV-2 variants. Recombinant viral receptor-binding domains (RBDs) are safe vaccine candidates but often have limited efficacy due to the lack of virus-like immunogen display pattern. Here we have developed a novel virus-like nanoparticle (VLP) vaccine that displays 120 copies of SARS-CoV-2 RBD on its surface. This VLP-RBD vaccine mimics virus-based vaccines in immunogen display, which boosts its efficacy while maintaining the safety of protein-based subunit vaccines. Compared to the RBD vaccine, the VLP-RBD vaccine induced five times more neutralizing antibodies in mice that efficiently blocked SARS- CoV-2 from attaching to its host receptor and potently neutralized the cell entry of various SARS-CoV-2 strains, SARS-CoV-1, and SARS-CoV-1-related bat coronavirus. These neutralizing immune responses induced by the VLP-RBD vaccine did not wane during a two-month study period. Furthermore, the VLP-RBD vaccine effectively protected mice from the SARS-CoV-2 challenge, dramatically reducing the development of clinical signs and pathological changes in immunized mice. The VLP-RBD vaccine provides one potentially effective solution to controlling the spread of SARS-CoV-2. In summary, the dissertation provides the structural basis for the receptor recognition of the SARS-CoV-2 variants of concern RBDs to human ACE2, and cross-species recognition of SARS-CoV-2 RBD to pangolin and mink ACE2s. The binding affinity determination and analysis of SARS-CoV-2 VOC RBDs and species-specific SARS-CoV-2 RBD mutations to cross-species ACE2s will help to elucidate the detailed interaction mechanism. Finally, the dissertation proposes and develops an effective novel virus-like particle vaccine against COVID-19.


University of Minnesota Ph.D. dissertation. July 2022. Major: Veterinary Medicine. Advisor: Fang Li. 1 computer file (PDF); xiii, 131 pages.

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Geng, Qibin. (2022). Receptor recognition of SARS-CoV-2 and vaccine design. Retrieved from the University Digital Conservancy,

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