Boston University School of Medicine, Department of Microbiology and National Infectious Diseases Laboratories, Boston, Massachusetts, USA.
Bioinformatics Program, Boston University, Boston, Massachusetts, USA.
mBio. 2020 Jun 16;11(3):e01157-20. doi: 10.1128/mBio.01157-20.
Outbreaks of filoviruses, such as those caused by the Ebola (EBOV) and Marburg (MARV) virus, are difficult to detect and control. The initial clinical symptoms of these diseases are nonspecific and can mimic other endemic pathogens. This makes confident diagnosis based on clinical symptoms alone impossible. Molecular diagnostics for these diseases that rely on the detection of viral RNA in the blood are only effective after significant disease progression. As an approach to identify these infections earlier in the disease course, we tested the effectiveness of viral RNA detection combined with an assessment of sentinel host mRNAs that are upregulated following filovirus infection. RNAseq analysis of EBOV-infected nonhuman primates identified host RNAs that are upregulated at early stages of infection. NanoString probes that recognized these host-response RNAs were combined with probes that recognized viral RNA and were used to classify viral infection both prior to viremia and postviremia. This approach was highly successful at identifying samples from nonhuman primate subjects and correctly distinguished the causative agent in a previremic stage in 10 EBOV and 5 MARV samples. This work suggests that unified host response/viral fingerprint assays can enable diagnosis of disease earlier than testing for viral nucleic acid alone, which could decrease transmission events and increase therapeutic effectiveness. Current molecular tests that identify infection with high-consequence viruses such as Ebola virus and Marburg virus are based on the detection of virus material in the blood. These viruses do not undergo significant early replication in the blood and, instead, replicate in organs such as the liver and spleen. Thus, virus begins to accumulate in the blood only after significant replication has already occurred in those organs, making viremia an indicator of infection only after initial stages have become established. Here, we show that a multianalyte assay can correctly identify the infectious agent in nonhuman primates (NHPs) prior to viremia through tracking host infection response transcripts. This illustrates that a single-tube, sample-to-answer format assay could be used to advance the time at which the type of infection can be determined and thereby improve outcomes.
丝状病毒（如埃博拉病毒 [EBOV] 和马尔堡病毒 [MARV]）的爆发难以检测和控制。这些疾病的初始临床症状是非特异性的，可能与其他地方性病原体相似。这使得仅根据临床症状进行明确诊断变得不可能。依赖于血液中病毒 RNA 检测的这些疾病的分子诊断仅在疾病进展到显著阶段后才有效。作为一种更早地在疾病过程中识别这些感染的方法，我们测试了结合检测丝状病毒感染后上调的哨兵宿主 mRNA 来检测病毒 RNA 的有效性。对感染埃博拉病毒的非人类灵长类动物的 RNAseq 分析确定了在感染早期上调的宿主 RNA。识别这些宿主反应 RNA 的 NanoString 探针与识别病毒 RNA 的探针相结合，并用于在病毒血症前和病毒血症后对病毒感染进行分类。这种方法在识别非人类灵长类动物样本方面非常成功，并在 10 个埃博拉病毒和 5 个马尔堡病毒样本中正确区分了潜伏期样本中的病原体。这项工作表明，统一的宿主反应/病毒指纹分析可以比单独检测病毒核酸更早地诊断疾病，从而减少传播事件并提高治疗效果。目前用于识别埃博拉病毒和马尔堡病毒等高后果病毒感染的分子检测基于血液中病毒物质的检测。这些病毒在血液中不会早期大量复制，而是在肝脏和脾脏等器官中复制。因此，只有在这些器官中已经发生了大量复制后，病毒才开始在血液中积累，使得病毒血症成为感染的指标，仅在初始阶段建立后。在这里，我们通过跟踪宿主感染反应转录本，显示在出现病毒血症之前，多分析物检测可以在非人类灵长类动物（NHP）中正确识别病原体。这表明，一种单管、样本到答案格式的检测可以用于提前确定感染类型，从而改善结果。
