An adjustable, safe and highly protective live-attenuated SARS-CoV-2 vaccine based on large-scale one-to-stop codon modifications

Abstract Vaccines are the most effective measure against COVID-19. However, novel and highly efficacious vaccines with simplified administration and broad immunogenicity, providing systemic and mucosal immunity are needed. Here, we show the development of live-attenuated vaccines (LAV) based on (i) recoding the SARS-CoV-2 genome to enrich for "one-to-stop" (OTS) codons, (ii) facilitating host responses by disabling non-structural-protein-1 (Nsp1) mediated translational repression, and deletion of open reading frames (ORF) 6, 7ab and 8, and (iii) deleting the spike polybasic cleavage site (PCS) to reduce LAV replication in the lung and prevent vaccine shedding. The OTS-modified SARS-CoV-2 LAV is adjustable regarding the level of attenuation, particularly vulnerable to mutagenic antiviral drugs, and protects efficiently against wild-type (WT) SARS-CoV-2 and recent variants of concern (VOC) in K18-hACE2 transgenic mice and Syrian hamsters. Furthermore, LAV immunization results in faster virus clearance after SARS-CoV-2 challenge compared to mRNA vaccines, a complete block of transmission of WT SARS-CoV-2, and significantly reduced transmission of Omicron BA.2 and BA.5 variants. Overall, the newly developed OTS-based LAVs represent a new generation of live vaccines that are intranasal administered at the natural site of infection, provide efficient and innovative infection control, and conceptionally are readily applicable to many other emerging viruses.