Temporally integrated transcriptome analysis reveals ASFV pathology and host response dynamics

African swine fever virus (ASFV) causes a lethal swine hemorrhagic disease and is currently responsible for widespread damage to the pig industry. The molecular mechanisms of ASFV pathogenicity and its interaction with host responses remain poorly understood. In this study, we profiled the temporal viral and host transcriptomes in porcine alveolar macrophages (PAMs) infected at 6, 12, 24 and 48 hours with highly virulent (SY18) and low virulent (HuB20) ASFV strains. We first identified profound differences in the virus expression programs between SY18 and HuB20, while the transcriptome dynamics in host cells were dominated by infection time. Through integrated computational analysis and experimental validation, we identified differentially expressed genes and related biological processes, and elaborated differential usage of the NF-kappaB related pathways by the two virus strains. In addition, we observed that compared to the highly virulent SY18 strain, HuB20 infection quickly activates expression of receptors, sensors, regulators, as well as downstream ef-fectors, including cGAS, STAT1/2, IRF9, MX1/2, suggesting rapid induction of a strong immune response. Lastly, we constructed a host-virus coexpression network, which shed light on pathogenic functions of several ASFV genes. Taken together, these results will provide a basis for further mechanistic studies on the functions of both viral and cellular genes that are involved in different responses.非洲猪瘟病毒（African swine fever virus, ASFV）可引发致死性猪出血性疾病，目前已给全球养猪业造成广泛重创。ASFV致病的分子机制及其与宿主免疫应答的相互作用，目前仍不甚明晰。本研究针对分别感染高毒力ASFV株（SY18）与低毒力ASFV株（HuB20）的猪肺泡巨噬细胞（porcine alveolar macrophages, PAMs），于感染后6、12、24及48小时四个时间点开展了时序病毒与宿主转录组图谱分析。研究首先发现，SY18与HuB20在病毒表达程序上存在显著差异，而宿主细胞的转录组动态变化则主要受感染时间调控。通过整合计算分析与实验验证，本研究筛选得到差异表达基因及其相关生物学过程，并阐明了两株病毒对NF-κB相关通路的差异化调控模式。此外，相较于高毒力株SY18，HuB20感染可快速激活受体、模式识别传感器、调控因子及其下游效应因子的表达，涵盖cGAS、STAT1/2、IRF9、MX1/2等，提示其可快速诱发强烈的免疫应答。最后，本研究构建了宿主-病毒共表达网络，为解析多个ASFV基因的致病功能提供了新的研究视角。综上，本研究结果可为后续深入探究参与不同感染应答的病毒与宿主基因的功能机制提供重要理论基础。