Dose-dependent effects of recombinant spike protein-based vaccination on SARS-CoV-2 evolutionary dynamics and the emergence of variants in hamster models

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to circulate globally through the persistent emergence of novel variants. Vaccination has been regarded as one of the selective environments that can influence SARS-CoV-2 evolution by exerting immune pressure. This study investigated the evolutionary dynamics of the SARS-CoV-2 Delta variant in hamsters immunized with varying doses of a full-length spike protein vaccine, potentially reflecting the heterogeneous levels of immunity. In hamster models, higher vaccine doses prevented viral replication in the lungs but only partially suppressed replication in the nasal passages. After excluding intra-host single-nucleotide variants (iSNVs) detected in non-vaccinated controls, a negative binomial model adjusting for read depth revealed a significant vaccine dose-dependent increase in iSNV occurrence in the Spike, ORF1a, ORF1b and ORF3a genes in nasal samples and positive selection signals were predominantly observed in the highest vaccine dose group. The iSNVs were observed in diverse and distinct combinations that were unique to each individual, reflecting host-specific intra-host mutation patterns. Some aa substitutions detected in at least two individuals in the vaccinated group were more frequently observed in the Omicron variant. In silico analyses incorporating individual-specific iSNVs demonstrated that reduced binding affinity to class 1 and 3 neutralizing antibodies was observed exclusively in variants identified from certain vaccinated individuals. In conclusion, these findings indicate that heterogeneous vaccine-induced immune pressure can shape intra-host SARS-CoV-2 evolution in a dose-dependent and host-specific manner and highlight the potential role of partial immunity and increased iSNVs in the upper respiratory tract in driving the emergence of putative immune-evasive viral variants.