The molecular processes that control flavivirus neurovirulence and drive their neuropathogenesis are currently unclear. This is in part due to the lack of the biologically relevant human model of flavivirus neuroinfection. To overcome this limitation, we previously established a human brain organoid (hBO) model of Zika virus (ZIKV) infection and used it to identify the role of viral noncoding RNA (sfRNA) in viral neuropathogenesis1. We have now built upon these results to develop a brain organoid model of West Nile virus (WNV) neuroinfection and employ it to dissect host processes in different types of brain cells during ZIKV and WNV infection.
Herein we also developed flavivirus-inclusive scRNA-Seq protocol and perform single-cell transcriptomic profiling of hBOs infected with WNV. We found that WNV predominantly infect neurons and only a small number of astrocytes, while ZIKV has a broad tropism to different cell types. Surprisingly, infected neurons did not express interferons (IFNs) and only ~1% of glial cells infected with either virus produced antiviral cytokines. Furthermore, infected and uninfected neurons developed little to no response to IFN as indicated by expression of interferon-stimulated genes (ISGs). Instead, they exhibited strong expression of the genes associated with autophagy and cell death. In contrast, profound IFN response was observed in astrocytes, radial glia and progenitor cells, which likely protected them from infection. Further gene expression analysis revealed that neurons lack expression of pattern recognition receptors, transcription factors or kinases required for antiviral signalling. These findings were confirmed by immunostaining of organoid sections and analysis of publicly available human brain scRNA-Seq datasets.
In conclusion, we demonstrated that neurons are vulnerable to flavivirus infection due to the lack of competency in pathogen sensing and IFN-response. Our data also suggests that apoptosis of the infected neurons and progenitor cells is it the likely cause of flavivirus neuropathogenesis.