Background: There is evidence for the protective effects of antibodies targeting non-structural protein 1 (NS1) of Zika virus (ZIKV); however, effective vaccines against ZIKV remain lacking. Methods: In this study, lipid nanoparticle (LNP)-encapsulated mRNA vaccines were designed based on the envelope domain III (EDIII) and NS1 sequences of the ZIKV FSS13025 strain, while protective efficacy was evaluated in a murine model using a ZIKV isolate obtained from Zhejiang Provincial Center for Disease Control and Prevention (Zhejiang CDC). Results: The vaccines were evaluated for key quality attributes—including particle size, polydispersity index (PDI), and encapsulation efficiency—as well as immunogenicity and protective efficacy. Both monovalent vaccine components exhibited uniform particle sizes (PDI < 0.2) and high encapsulation efficiencies (≥80%) and induced high levels of antigen-specific antibodies in mice in a dose-dependent manner. The EDIII mRNA vaccine elicited moderate ZIKV-neutralizing antibody titers as measured by PRNT50, whereas the NS1 vaccine did not induce detectable neutralizing antibodies. Both bicomponent (EDIII + NS1) mRNA vaccines induced a Th1-biased cellular immune response in mouse splenocytes, with significantly greater IFN-γ production compared with either monovalent vaccine. In viral challenge experiments using 1 × 105 PFU ZIKV (Zhejiang CDC isolate, intraperitoneal), the bicomponent vaccine provided complete protection, with 100% survival across all dose groups. In contrast, the EDIII and NS1 monovalent vaccines showed partial protection: mortality was observed in the 20 μg dose groups and exceeded 50% in the 10 μg dose groups. Conclusions: These results demonstrate that the bicomponent EDIII + NS1 mRNA vaccine combination confers superior protective efficacy compared with either component alone, consistent with a synergistic effect between humoral and cellular immune responses. This study provides a novel strategy for next-generation Zika vaccine development.
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