Single-cell virus sequencing of influenza infections that trigger innate immunity

Influenza-infected cells vary widely in their expression of viral genes, and only occasionally activate innate immunity. Here we develop a new method to assess how the genetic variation in viral populations contributes to this heterogeneity. We do this by determining the transcriptome and full-length sequences of all viral genes in single cells infected with a nominally \"pure\" stock of influenza virus. Most cells are infected by virions with defects, some of which increase the frequency of innate-immune activation. These immunostimulatory defects are diverse, and include mutations that perturb the function of the viral polymerase protein PB1, large internal deletions in viral genes, and failure to express the virus's interferon antagonist NS1. However, immune activation remains stochastic in cells infected by virions with these defects, and occasionally is triggered even by virions that express unmutated copies of all genes. Our work shows that the diverse spectrum of defects in influen...

感染流感病毒的细胞在病毒基因的表达层面存在显著异质性，且仅会偶尔激活先天免疫（innate immunity）通路。本研究开发了一种全新方法，用以解析病毒种群的遗传变异如何介导这种细胞异质性。我们通过对感染名义上"纯"毒株原液的流感病毒的单个细胞内的转录组（transcriptome）与所有病毒基因的全长序列进行测序分析，达成该研究目标。多数细胞被携带缺陷的病毒粒子（virion）感染，其中部分缺陷可提升先天免疫激活的发生频率。这类具有免疫激活效应的病毒缺陷类型多样，包括扰乱病毒聚合酶蛋白PB1功能的突变、病毒基因内部大片段缺失，以及无法表达病毒的干扰素拮抗蛋白NS1。不过，即便感染携带上述缺陷的病毒粒子，细胞的免疫激活仍呈现随机特性；甚至部分仅携带全部基因均未突变的病毒粒子感染的细胞，也会偶尔触发免疫激活。本研究表明，流感病毒种群中存在的多样化缺陷谱……