Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
Department of Analytical, Physical, and Social Sciences, Carlow University, Pittsburgh, PA, USA.
J Theor Biol. 2022 Jan 7;532:110918. doi: 10.1016/j.jtbi.2021.110918. Epub 2021 Sep 27.
Respiratory viral infections pose a serious public health concern, from mild seasonal influenza to pandemics like those of SARS-CoV-2. Spatiotemporal dynamics of viral infection impact nearly all aspects of the progression of a viral infection, like the dependence of viral replication rates on the type of cell and pathogen, the strength of the immune response and localization of infection. Mathematical modeling is often used to describe respiratory viral infections and the immune response to them using ordinary differential equation (ODE) models. However, ODE models neglect spatially-resolved biophysical mechanisms like lesion shape and the details of viral transport, and so cannot model spatial effects of a viral infection and immune response. In this work, we develop a multiscale, multicellular spatiotemporal model of influenza infection and immune response by combining non-spatial ODE modeling and spatial, cell-based modeling. We employ cellularization, a recently developed method for generating spatial, cell-based, stochastic models from non-spatial ODE models, to generate much of our model from a calibrated ODE model that describes infection, death and recovery of susceptible cells and innate and adaptive responses during influenza infection, and develop models of cell migration and other mechanisms not explicitly described by the ODE model. We determine new model parameters to generate agreement between the spatial and original ODE models under certain conditions, where simulation replicas using our model serve as microconfigurations of the ODE model, and compare results between the models to investigate the nature of viral exposure and impact of heterogeneous infection on the time-evolution of the viral infection. We found that using spatially homogeneous initial exposure conditions consistently with those employed during calibration of the ODE model generates far less severe infection, and that local exposure to virus must be multiple orders of magnitude greater than a uniformly applied exposure to all available susceptible cells. This strongly suggests a prominent role of localization of exposure in influenza A infection. We propose that the particularities of the microenvironment to which a virus is introduced plays a dominant role in disease onset and progression, and that spatially resolved models like ours may be important to better understand and more reliably predict future health states based on susceptibility of potential lesion sites using spatially resolved patient data of the state of an infection. We can readily integrate the immune response components of our model into other modeling and simulation frameworks of viral infection dynamics that do detailed modeling of other mechanisms like viral internalization and intracellular viral replication dynamics, which are not explicitly represented in the ODE model. We can also combine our model with available experimental data and modeling of exposure scenarios and spatiotemporal aspects of mechanisms like mucociliary clearance that are only implicitly described by the ODE model, which would significantly improve the ability of our model to present spatially resolved predictions about the progression of influenza infection and immune response.
呼吸道病毒感染是一个严重的公共卫生问题,包括轻度季节性流感和 SARS-CoV-2 等大流行。病毒感染的时空动态几乎影响病毒感染进展的各个方面,例如病毒复制率对细胞和病原体类型的依赖性、免疫反应的强度以及感染的定位。数学模型通常用于使用常微分方程 (ODE) 模型来描述呼吸道病毒感染和对它们的免疫反应。然而,ODE 模型忽略了空间分辨的生物物理机制,例如病变形状和病毒运输的细节,因此无法模拟病毒感染和免疫反应的空间效应。在这项工作中,我们通过结合非空间 ODE 建模和基于细胞的空间建模来开发流感感染和免疫反应的多尺度、多细胞时空模型。我们采用细胞化(cellularization),这是一种最近开发的从非空间 ODE 模型生成空间、基于细胞的随机模型的方法,从描述感染、易感细胞的死亡和恢复以及固有和适应性反应的已校准 ODE 模型生成我们模型的大部分内容在流感感染期间,以及开发细胞迁移和 ODE 模型未明确描述的其他机制的模型。我们确定了新的模型参数,以在某些条件下在空间和原始 ODE 模型之间生成一致性,其中使用我们的模型的模拟副本作为 ODE 模型的微配置,并且比较模型之间的结果以研究病毒暴露的性质和异质感染对病毒感染的时间演化的影响。我们发现,使用与 ODE 模型校准期间使用的空间均匀初始暴露条件一致的条件会产生较轻的感染,并且局部暴露于病毒的程度必须比均匀应用于所有可用的易感细胞的暴露程度高出多个数量级。这强烈表明暴露的本地化在甲型流感感染中起着重要作用。我们提出,病毒引入的微环境的特殊性在疾病发作和进展中起着主导作用,并且像我们这样的空间分辨模型可能对于基于潜在病变部位的易感性使用基于感染状态的患者的空间分辨数据更好地理解和更可靠地预测未来的健康状态很重要。我们可以轻松地将我们模型的免疫反应组件集成到其他病毒感染动力学建模和模拟框架中,这些框架对病毒内化和细胞内病毒复制动力学等其他机制进行详细建模,而这些机制在 ODE 模型中并未明确表示。我们还可以将我们的模型与现有的暴露场景实验数据和建模以及对黏液纤毛清除等机制的时空方面进行组合,这些方面仅在 ODE 模型中隐含描述,这将显著提高我们的模型预测流感感染和免疫反应进展的空间分辨能力。
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