关于细胞质RNA病毒（如冠状病毒）的RNA-RNA相互作用是否会产生假定的病毒源小RNA（miRNA样分子）的生物发生，存在争议。更重要的是，关于野生动物病毒的RNA-RNA相互作用是否会作为病毒源小RNA的问题尚不清楚。在这里，我们采用四种方法来解决这些问题。首先，我们使用在不同蝙蝠物种、中间宿主和人类寄主中循环的SARS-CoV、MERS-CoV和SARS-CoV-2基因组中经过负选择的保守RNA结构。其次，我们进行了系统性的文献回顾，以确定与β冠状病毒靶向有关的人类hsa-miRNAs与肺细胞感染的关系。第三，我们利用先进的长程RNA-RNA相互作用来改进hsa-miRNAs与保守RNA结构的种子序列同源性。第四，我们利用高通量RNA测序技术对β冠状病毒感染的上皮肺癌细胞系（Calu-3）进行验证。我们提出了九个可能的病毒源小RNAs：两个SARS-CoV的vsRNAs（蝙蝠：SB-vsRNA-ORF1a-3p；SB-vsRNA-S-5p），一个MERS-CoV的vsRNA（蝙蝠：MB-vsRNA-ORF1b-3p），以及六个SARSCoV-2的vsRNAs（蝙蝠：S2B-vsRNA-ORF1a-5p；中间宿主：S2I-vsRNA-ORF1a-5p；人类：S2H-vsRNA-ORF1a-5p，S2H-vsRNA-ORF1a-3p，S2H-vsRNA-ORF1b-3p，S2H-vsRNA-ORF3a-3p），主要由非结构蛋白3编码。值得注意的是，β冠状病毒源小RNAs靶向了74个在感染人类细胞中不同表达的基因，其中55个上调分子机制可能与急性呼吸窘迫综合征（ARDS）相关，而19个下调的基因可能与神经营养因子信号传导受损有关。这些结果揭示了一种新的基于小RNA的调控机制参与了神经病理发生，需要进一步研究以验证其治疗应用。

Whether RNA-RNA interactions of cytoplasmic RNA viruses, such as Betacoronavirus, might end in the biogenesis of putative virus-derived small RNAs as miRNA-like molecules has been controversial. Even more, whether RNA-RNA interactions of wild animal viruses may act as virus-derived small RNAs is unknown. Here, we address these issues in four ways. First, we use conserved RNA structures undergoing negative selection in the genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 circulating in different bat species, intermediate animals, and human hosts. Second, a systematic literature review was conducted to identify Betacoronavirus-targeting hsa-miRNAs involved in lung cell infection. Third, we employed sophisticated long-range RNA-RNA interactions to refine the seed sequence homology of hsa-miRNAs with conserved RNA structures. Fourth, we used high-throughput RNA sequencing of a Betacoronavirus-infected epithelial lung cancer cell line (Calu-3) to validate the results. We proposed nine potential virus-derived small RNAs: two vsRNAs in SARS-CoV (Bats: SB-vsRNA-ORF1a-3p; SB-vsRNA-S-5p), one vsRNA in MERS-CoV (Bats: MB-vsRNA-ORF1b-3p), and six vsRNAs in SARS-CoV-2 (Bats: S2B-vsRNA-ORF1a-5p; intermediate animals: S2I-vsRNA-ORF1a-5p; and humans: S2H-vsRNA-ORF1a-5p, S2H-vsRNA-ORF1a-3p, S2H-vsRNA-ORF1b-3p, S2H-vsRNA-ORF3a-3p), mainly encoded by nonstructural protein 3. Notably, Betacoronavirus-derived small RNAs targeted 74 differentially expressed genes in infected human cells, of which 55 upregulate the molecular mechanisms underlying acute respiratory distress syndrome (ARDS), and the 19 downregulated genes might be implicated in neurotrophin signaling impairment. These results reveal a novel small RNA-based regulatory mechanism involved in neuropathogenesis that must be further studied to validate its therapeutic use.