摘要近年来，新型冠状病毒肺炎、流行性感冒、埃博拉出血热等病毒性疾病呈现愈演愈烈、愈发愈快的趋势。为保障人民健康和国民经济的稳定运行，研究病毒的致病机理与宿主免疫调控机制，解析病毒与宿主的基因表达调控规律，监测病原病毒与防治病毒病的重要性逐渐凸显。转录组测序是一类在RNA水平上关注基因在特定时空状态下表达特征的技术，是分析差异基因表达和研究mRNA差异剪接必不可少的工具。随着分子生物学实验技术的进步和生物信息学分析平台的成熟，转录组学研究向着低成本、低技术门槛的方向发展，逐渐从理论研究领域向临床实验室过渡，改变着临床工作人员对病毒与病毒病的传统认知，被越来越多的用于病毒转录机制、病毒与宿主的免疫互作、追踪疾病进展以及抗病毒药物研发等方面研究。本文主要对宏转录组的技术流程、常用软件以及病毒与病毒病方向的应用场景进行综述，并对细胞群转录组、单细胞转录组、单细胞核转录组以及空间转录组的方法与应用进行简要介绍，以期为病毒转录机制研究与病毒病的防控提供方法学参考。

abstractsFor the past few years, viral diseases such as Coronavirus Disease 2019, Influenza, and Ebola hemorrhagic fever have become more severe and more frequent. For people’s health and the stable operation of the national economy, it is of increasing importance to research the pathogenesis of virus and host immune regulation mechanism, analyze the regulation of gene expression between virus and host, and surveil pathogenic viruses and prevent virus diseases. Transcriptome sequencing is a kind of technology at the RNA level that focuses on the expression characteristics of genes in a specific space-time state, and it is an indispensable tool for analyzing differential gene expression and researching differential splicing of mRNA. With the progress of molecular biology experimental technology and the maturity of bioinformatics analysis platforms, transcriptomics is developing towards the low-cost and low technical threshold, which is gradually transitioning from the research field to the clinical laboratory and changing the traditional cognition of clinical staff in viruses and viral diseases. It has been increasingly used in the research of viral transcription mechanisms, immune interaction between virus and host, tracking disease progression, and antiviral drug development. In order to provide a methodological reference for the research of virus mechanism and prevention and control of virus disease, here, we mainly review meta-transcriptome from three aspects: technical process, common software and application scenarios of virus and virus diseases, and briefly mention the method and applications of other transcriptomes, including a population of cells RNA sequencing (Bulk RNA-seq), Single-cell RNA sequencing (ScRNA-seq), Single-nuclear RNA sequencing (SnRNA-seq), and Spatial Transcriptome (ST).