Larkin Caroline I, Dunn Matthew D, Shoemaker Jason E, Klimstra William B, Faeder James R
Joint Carnegie Mellon University - University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America.
Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
bioRxiv. 2024 Dec 26:2024.12.13.628424. doi: 10.1101/2024.12.13.628424.
Eastern equine encephalitis virus (EEEV) is an arthropod-borne, positive-sense RNA alphavirus posing a substantial threat to public health. Unlike similar viruses such as SARS-CoV-2, EEEV replicates efficiently in neurons, producing progeny viral particles as soon as 3-4 hours post-infection. EEEV infection, which can cause severe encephalitis with a human mortality rate surpassing 30%, has no licensed, targeted therapies, leaving patients to rely on supportive care. Although the general characteristics of EEEV infection within the host cell are well-studied, it remains unclear how these interactions lead to rapid production of progeny viral particles, limiting development of antiviral therapies. Here, we present a novel rule-based model that describes attachment, entry, uncoating, replication, assembly, and export of both infectious virions and virus-like particles within mammalian cells. Additionally, it quantitatively characterizes host ribosome activity in EEEV replication via a model parameter defining ribosome density on viral RNA. To calibrate the model, we performed experiments to quantify viral RNA, protein, and infectious particle production during acute infection. We used Bayesian inference to calibrate the model, discovering in the process that an additional constraint was required to ensure consistency with previous experimental observations of a high ratio between the amounts of full-length positive-sense viral genome and negative-sense template strand. Overall, the model recapitulates the experimental data and predicts that EEEV rapidly concentrates host ribosomes densely on viral RNA. Dense packing of host ribosomes was determined to be critical to establishing the characteristic positive to negative RNA strand ratio because of its role in governing the kinetics of transcription. Sensitivity analysis identified viral transcription as the critical step for infectious particle production, making it a potential target for future therapeutic development.
东部马脑炎病毒（EEEV）是一种节肢动物传播的正链RNA甲病毒，对公众健康构成重大威胁。与SARS-CoV-2等类似病毒不同，EEEV在神经元中能高效复制，感染后3至4小时即可产生子代病毒颗粒。EEEV感染可导致严重脑炎，人类死亡率超过30%，目前尚无经许可的靶向治疗方法，患者只能依赖支持性护理。尽管宿主细胞内EEEV感染的一般特征已得到充分研究，但尚不清楚这些相互作用如何导致子代病毒颗粒的快速产生，这限制了抗病毒疗法的发展。在此，我们提出了一种基于规则的新型模型，该模型描述了哺乳动物细胞内传染性病毒粒子和病毒样颗粒的附着、进入、脱壳、复制、组装和输出。此外，它通过定义病毒RNA上核糖体密度的模型参数，定量表征了宿主核糖体在EEEV复制中的活性。为了校准该模型，我们进行了实验，以量化急性感染期间病毒RNA、蛋白质和传染性颗粒的产生。我们使用贝叶斯推理来校准模型，在此过程中发现需要一个额外的约束条件，以确保与之前关于全长正链病毒基因组与负链模板链数量高比例的实验观察结果一致。总体而言，该模型概括了实验数据，并预测EEEV会迅速将宿主核糖体密集地聚集在病毒RNA上。由于宿主核糖体的密集堆积在控制转录动力学方面的作用，它被确定为建立特征性正链与负链RNA比例的关键因素。敏感性分析确定病毒转录是传染性颗粒产生的关键步骤，使其成为未来治疗开发的潜在靶点。
