Although mRNA-based COVID-19 vaccines have demonstrated high efficacy, their widespread global use remains constrained by high production costs and cold-chain requirements. Modified vaccinia virus Ankara (MVA) is a highly attenuated and thermostable viral vector with low production costs, potent immunogenicity, and strong potential for global distribution. Here, we compared head-to-head the long-term immunogenicity and efficacy of an MVA-based vaccine candidate with an approved mRNA vaccine in K18-hACE2 mice, both expressing the SARS-CoV-2 Omicron XBB.1.5 spike (S) protein. Mice received by intramuscular route homologous (mRNA/mRNA and MVA/MVA), heterologous (mRNA/MVA), or single-dose MVA regimens. SARS-CoV-2-specific humoral and cellular responses were evaluated at 10 days and 9 months after the last vaccination, as well as antibody levels at intermediate time points, and protection was assessed following intranasal SARS-CoV-2 XBB.1.5 challenge at 9 months post-vaccination. Binding IgG antibodies against the XBB.1.5 S protein remained high throughout the 9-month period in all vaccinated groups, whereas neutralizing antibody titers peaked early after the last vaccination and progressively declined, converging across regimens over time. S-specific CD8+ T-cell responses were strongest in mRNA-containing regimens at day 10 after the last vaccination and, although they contracted over time, they remained detectable at 9 months after the last vaccination in all two-dose groups, with a trend toward enhanced persistence in the heterologous mRNA/MVA regimen. In contrast, S-specific CD4+ T-cell responses remained low across all groups. All two-dose regimens markedly reduced viral RNA levels and infectious viral titers in both the upper and lower respiratory tract following SARS-CoV-2 XBB.1.5 challenge. Transcriptomic analysis of lung tissue after virus challenge revealed reduced expression of genes associated with inflammatory myeloid responses, interferon signalling and cellular stress in vaccinated mice compared with infected controls. Distinct post-challenge lung transcriptional profiles were observed across vaccination regimens, with differential modulation of genes associated with humoral, innate, and cellular immune responses. Overall, our findings demonstrate that MVA-based vaccination induces durable immunity in mice and achieves long-term control of SARS-CoV-2 XBB.1.5 replication comparable to that of mRNA vaccination, supporting its use as an alternative and complementary vaccine platform against SARS-CoV-2 and other emerging respiratory viruses.
