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New variants of SARS-CoV-2 are continually emerging with mutations in spike associated with increased transmissibility and immune escape. Phenotypic maps can inform the prediction of concerning mutations from genomic surveillance, however most of these maps currently derive from studies using monomeric RBD, while spike is trimeric, and contains additional domains. These maps may fail to reflect interdomain interactions in the prediction of phenotypes. To try to improve on this, we developed a platform for deep mutational scanning using whole trimeric spike. We confirmed a previously reported epistatic effect within the RBD affecting ACE2 binding, that highlights the importance of updating the base spike sequence for future mutational scanning studies. Using post vaccine sera, we found that the immune response of vaccinated individuals was highly focused on one or two epitopes in the RBD and that single point mutations at these positions can account for most of the immune escape mediated by the Omicron BA.1 RBD. However, unexpectedly we found that the BA.1 RBD alone does not account for the high level of antigenic escape by BA.1 spike. We show that the BA.1 NTD amplifies the immune evasion of its associated RBD. BA.1 NTD reduces neutralistion by RBD directed monoclonal antibodies, and impacts ACE2 interaction. NTD variation is thus an important mechanism of immune evasion by SARS-CoV-2. Such effects are not seen when pre-stabilized spike proteins are used, suggesting the interdomain effects require protein mobility to express their phenotype. Author summary: SARS-CoV-2 continues to evolve into new variants bearing RBD and NTD mutations in spike that confer immune escape. Phenotypic maps of SARS-CoV-2 spike mutations used in surveillance and forecasting are based largely on data using screens with monomeric RBD, rather than trimeric whole spike. Interactions between the NTD and RBD affect receptor binding affinity and immune escape of the SARS-CoV-2 spike. Using deep mutational scanning with whole trimeric spike, we identified antibody escape mutations that have subsequently emerged in nature. Vaccine responses were found to be focused on one or two epitopes, making immune escape possible with single mutations. Because we used whole spike, we uncovered an unexpected role for the NTD in enhancing antibody escape from RBD directed antibodies. Genomic surveillance should take account of this new role of the NTD when scanning for VOCs. [ABSTRACT FROM AUTHOR]

Vaccines for SARS-CoV-2 have been hugely successful in alleviating hospitalization and deaths caused by the newly emerged coronavirus that is the cause of COVID. However, although the parentally administered vaccines are very effective at reducing severe disease, they do not induce sterilizing immunity. As the virus continues to circulate around the globe, it is still not clear how long protection will last, nor whether variants will emerge that escape vaccine immunity. Animal models can be useful to complement studies of antigenicity of novel variants and inform decision making about the need for vaccine updates. The Syrian golden hamster is the preferred small animal model for SARS-CoV-2 infection. Since virus is efficiently transmitted between hamsters, we developed a transmission challenge model that presents a more natural dose and route of infection than the intranasal challenge usually employed. Our studies demonstrate that an saRNA vaccine based on the earliest Wuhan-like virus spike sequence induced neutralizing antibodies in sera of immunized hamsters at similar titres to those in human convalescent sera or vaccine recipients. The saRNA vaccine was equally effective at abrogating clinical signs in animals who acquired through exposure to cagemates infected either with a virus isolated in summer 2020 or with a representative Alpha (B.1.1.7) variant isolated in December 2020. The vaccine also reduced shedding of infectious virus from the nose, further reinforcing its likely effectiveness at reducing onwards transmission. This model can be extended to test the effectiveness of vaccination in blocking infections with and transmission of novel variants as they emerge. [ABSTRACT FROM AUTHOR]