Karamitros Timokratis, Pogka Vasiliki, Papadopoulou Gethsimani, Tsitsilonis Ourania, Evangelidou Maria, Sympardi Styliani, Mentis Andreas
Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
Bioinformatics and Applied Genomics Unit, Hellenic Pasteur Institute, 11521 Athens, Greece.
Microorganisms. 2021 Jul 20;9(7):1538. doi: 10.3390/microorganisms9071538.
Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host-pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy.
麻疹病毒（MeV）具有一个长度为15 kb的负链RNA基因组，该基因组通常是保守的。高通量测序（HTS）和双RNA测序的最新进展使得通过同时表征宿主转录组来分析病毒RNA基因组并发现病毒感染生物标志物成为可能。然而，在MeV感染中，这些宿主-病原体相互作用在很大程度上仍未得到探索。我们对6例经常规实时PCR检测确诊为MeV感染患者的咽拭子标本和6例外周血单核细胞（PBMC）标本进行了非靶向双RNA测序。在对总核酸进行优化的DNA酶处理后，我们使用咽拭子样本构建了富含多聚腺苷酸的NGS文库。我们利用咽拭子数据集重建了病毒基因组，并进一步进行差异表达、基因本体和通路富集分析，以比较MeV感染患者与健康个体对照组的咽拭子和外周血转录组。我们获得了6个MeV B3基因型的全基因组序列。我们仔细分析了MeV感染的咽上皮细胞的转录组，检测到了所有已知的病毒感染生物标志物，还揭示了一组局部抗病毒和炎症免疫反应的功能簇，这与在PBMC转录组中观察到的反应有很大不同。双RNA测序技术在MeV感染患者中的应用有可能提供有关病毒基因组结构和细胞固有免疫反应的有价值信息，并推动抗病毒治疗新靶点的发现。
