Newcastle disease virus (NDV) is a contagious poultry paramyxovirus, leading to substantial economic losses to the poultry industry. Here, RNA-seq was carried out to investigate the altered expression of immune-related genes in chicken thymus within 96 h in response to NDV infection. In NDV-infected chicken thymus tissues, comparative transcriptome analysis revealed 1386 differentially expressed genes (DEGs) at 24 h with 989 up- and 397 down-regulated genes, 728 DEGs at 48 h with 567 up- and 161 down-regulated genes, 1514 DEGs at 72 h with 1016 up- and 498 down-regulated genes, and 1196 DEGs at 96 h with 522 up- and 674 down-regulated genes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these candidate targets mainly participate in biological processes or biochemical, metabolic and signal transduction processes. Notably, there is large enrichment in biological processes, cell components and metabolic processes, which may be related to NDV pathogenicity. In addition, the expression of five immune-related DEGs identified by RNA-seq was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our results indicated that the expression levels of AvBD5, IL16, IL22 and IL18R1 were obviously up-regulated, and Il-18 expression was also changed, but not significantly, which play key roles in the defense against NDV. Overall, we identified several candidate targets that may be involved in the regulation of NDV infection, which provide new insights into the complicated regulatory mechanisms of virus-host interactions, and explore new strategies for protecting chickens against the virus.

新城疫病毒（NDV）是一种具有传染性的家禽副粘病毒，对家禽业造成巨大的经济损失。在这里，进行了RNA-seq研究，以响应NDV感染在96小时内改变鸡胸腺中免疫相关基因的表达。在NDV感染的鸡胸腺组织中，比较转录组分析显示24小时有1386个差异表达基因（DEG），其中989个上调基因和397个下调基因，48小时有728个DEGs，其中567个上调基因和161个下调基因，1514年在72小时的DEG分别具有1016个上调和498个下调的基因，以及在1个96个小时时具有522个上调和674个下调的基因。基因本体论（GO）和《京都基因与基因组百科全书》（KEGG）分析表明，这些候选目标主要参与生物过程或生化过程，代谢和信号转导过程。值得注意的是，生物过程，细胞成分和代谢过程中大量富集，这可能与NDV的致病性有关。另外，通过定量实时聚合酶链反应（qRT-PCR）验证了通过RNA-seq鉴定的五个免疫相关DEG的表达。我们的结果表明，AvBD5，IL16，IL22和IL18R1的表达水平明显上调，Il-18的表达也发生了变化，但没有明显变化，这在抗NDV中起关键作用。总体而言，我们确定了可能参与NDV感染调控的几个候选靶标，这些靶标提供了对病毒-宿主相互作用的复杂调控机制的新见解，并探索了保护鸡只免受病毒感染的新策略。