Zika virus infections of human stem cell-derived cerebral organoids reveal viral lineage-specific pathogenesis responses

Zika virus (ZIKV) has multiple lineages and strains that cause a range of disease severity, underscoring the need to elucidate differential neuropathogenesis mechanisms. Here, we performed systematic, side-by-side comparisons of African, Asian, and American ZIKV lineage infections using cerebral organoids derived from human embryonic stem cells, a relevant human model experimental system. African lineage ZIKV strains, as well as the ancestral Asian Malaysia strain, persistently infected neural progenitor cells, causing apoptosis and severe disruption of ventricular cytoarchitecture. In contrast, contemporary Asian and American lineage viruses were cleared from ventricles, coinciding with low apoptosis and reduced neuropathology. Single-cell RNA sequencing demonstrated upregulated cell-type-specific antiviral signaling during American lineage infections, coinciding with viral clearance from ventricular progenitor cells. Conversely, pathogenic African lineage infections were associated with apoptosis, reduced STAT2 and IFIT1 protein levels, and enhanced activation of stress pathways. African lineage and ancestral Malaysian strain infections induced mitochondrial oxidative stress. Scavenging the reactive oxygen species improved ventricular cytoarchitecture and progenitor survival, but without reducing viral titers. Together, these findings suggest that lineage- and strain-specific host stress responses, rather than viral burden alone, contribute to ZIKV-induced neurodevelopmental damage. An implication of this study is that host-directed therapeutic strategies, used to improve host tolerance to viral infection, may benefit clinical outcomes. IMPORTANCE: This study provides a systematic comparison of Zika virus (ZIKV) lineage infections in a relevant human model system to correlate mechanisms of host cellular responses with neuropathogenesis. By analyzing African, Asian, and American ZIKV infections side by side in cerebral organoids derived from human embryonic stem cells, we link persistent infection of neural progenitor cells to elevated cellular stress responses and structural disruption of organoid ventricles. Structural disruption was reduced by adding a hydroxyl radical scavenger, but without lowering viral titer. These data are important in strongly suggesting that host responses to viral infection can be of equal or greater importance than viral burden in determining pathogenesis. This study provides mechanistic insight into how closely related viral lineage infections result in divergent outcomes in the developing brain. The data have added importance for suggesting the potential value of host-directed therapeutics to improve ZIKV tolerance without addressing viral titer.