Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics (InVivo scRNA-seq). Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics (InVivo scRNA-seq)

Ebola virus (EBOV) causes epidemics with high mortality, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, providing insight into pathogenesis: e.g., immature, proliferative monocyte-lineage cells with reduced antigen presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV down-regulates STAT1 mRNA and interferon signaling, and up-regulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response, and provides a framework for characterizing host-virus interactions under maximum containment. Overall design: Single-cell RNA-Seq analysis of circulating immune cells transcriptomes in a rhesus macaque in vivo Ebola infection model at multiple days post innoculation.

埃博拉病毒（Ebola virus, EBOV）可引发高致死率疫情，但由于高生物安全等级实验室及暴发场景下的实验操作难度极大，该病毒的相关研究仍相对不足。本研究借助单细胞转录组学（single-cell transcriptomics）与基于质谱流式细胞术（CyTOF）的单细胞蛋白定量技术，对恒河猴感染埃博拉病毒期间的外周免疫细胞进行系统性特征解析。本次研究共获取10万条转录组数据与1500万条蛋白谱数据，为埃博拉病毒的致病机制提供了关键见解：例如，抗原呈递能力受损的未成熟增殖性单核细胞谱系细胞替代了常规单核细胞亚群；同时淋巴细胞上调凋亡相关基因的表达，且细胞丰度显著降低。通过对细胞内病毒RNA进行定量分析，本研究鉴定出循环免疫细胞的病毒嗜性分子决定因子，并解析了病毒与宿主基因表达的时序动态变化规律。在受感染细胞内，埃博拉病毒可下调STAT1 mRNA的表达与干扰素信号通路活性，并上调潜在的促病毒基因（如DYNLL1与HSPA5）的表达，从而明确了病毒为实现自身复制所操控的核心信号通路。本研究揭示了埃博拉病毒的嗜性特征、复制动态及诱发的免疫应答，并为最高生物安全管控条件下宿主-病毒互作的特征解析提供了标准化研究框架。整体实验设计：在恒河猴体内埃博拉病毒感染模型中，对接种后多个时间点的循环免疫细胞转录组开展单细胞RNA测序（Single-cell RNA-Seq）分析。