Comparison of human cerebral organoids infected with wild-type Zika versus attenuated DN-2 virus strains uncovers differences in host immune responses.

Zika virus (ZIKV), a neurotropic virus, poses significant global health challenges because of its ability to cause severe neurological complications and congenital brain abnormalities. Prenatal ZIKV infection impairs early brain development. However, details of the molecular mechanisms driving their virulence remain incompletely understood. Here, we performed comparatively analyses of infection outcomes caused by 2 different ZIKV strains - wild-type (WT) ZIKV versus an attenuated strain (DN-2) - in human cerebral organoids (hCOs) to dissect host responses that could contribute to pathogenicity. Although both viral strains productively infected hCOs with indiscernible gross pathological changes, differences in host responses and subtypes of cells infected discriminate WT ZIKV from DN-2 infections. Single cell RNA sequencing analyses uncovered differently expressed genes (DEGs) that were common to both virus strains, as well as DEGs that were specific to either WT ZIKV or DN-2. For common DEGs, WT ZIKV infections elicited stronger expression of key genes involved in host immune response pathways, such as IFIT2, DDX60, OAS1 and XAF1. Moreover, analyses of WT ZIKV-specific upregulated DEGs uncovered mobilisation of additional innate immune response pathways not found in DN-2. Additionally, while WT ZIKV infected a broad range of cell types in hCOs, DN-2 infections were predominantly limited to radial glial, which are neuroprogenitors essential for neurogenesis. These results highlight that differences in host immune responses and tropism distinguish neurotropic WT ZIKV and attenuated DN-2 infections, underscoring the mechanistic differences involved in pathogenicity. Our study provides further insights into mechanisms used by neurotrophic ZIKV to drive neuropathogenesis during infection of the developing brain.