Manipulating Zika virus RNA tertiary structure for developing tissue-specific attenuated vaccines

Traditional live attenuated vaccines (LAVs) are typically developed through serial passaging or genetic engineering to introduce specific mutations or deletions. While viral RNA secondary or tertiary structures have been well-documented for their multiple functions, including binding with specific host proteins, their potential for LAV design remains largely unexplored. Herein, using Zika virus (ZIKV) as a model, we demonstrate that targeted disruption of the primary sequence or tertiary structure of a specific viral RNA element responsible for Musashi-1 (MSI1) binding leads to a tissue-specific attenuation phenotype in multiple animal models. The engineered MSI1-binding-deficient ZIKV mutants (MBD) maintained full competence in MSI1-deficient tissues but were significantly restricted in ZIKV-vulnerable tissues (brain, testis, eye and placenta) and exhibited substantially reduced vertical transmission in mice. Importantly, a single immunization with MBD ZIKV induced robust immune responses and conferred protection against ZIKV challenge in both mice and non-human primates. Thus, our study demonstrates that manipulating viral RNA structures that interact with host proteins represents a powerful platform for developing the next generation of LAVs against emerging viruses.