Eco-evolutionary dynamics of pathogen immune-escape: deriving a population-level phylodynamic curve.

IF 3.7 2区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES
Journal of The Royal Society Interface Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI:10.1098/rsif.2024.0675
Bjarke Frost Nielsen, Chadi M Saad-Roy, C Jessica E Metcalf, Cécile Viboud, Bryan T Grenfell
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引用次数: 0

Abstract

The phylodynamic curve (Grenfell et al. 2004 Science 303, 327-332 (doi:10.1126/science.1090727)) conceptualizes how immunity shapes the rate of viral adaptation in a non-monotonic fashion, through its opposing effects on viral abundance and the strength of selection. However, concrete and quantitative model realizations of this influential concept are rare. Here, we present an analytic, stochastic framework in which a population-scale phylodynamic curve emerges dynamically, allowing us to address questions regarding the risk and timing of the emergence of viral immune escape variants. We explore how pathogen- and population-specific parameters such as strength of immunity, transmissibility, seasonality and antigenic constraints affect the emergence risk. For pathogens exhibiting pronounced seasonality, we find that the timing of likely immune-escape variant emergence depends on the level of case importation between regions. Motivated by the COVID-19 pandemic, we probe the likely effects of non-pharmaceutical interventions (NPIs), and the lifting thereof, on the risk of viral escape variant emergence. Looking ahead, the framework has the potential to become a useful tool for probing how natural immunity, as well as choices in vaccine design and distribution and the implementation of NPIs, affect the evolution of common viral pathogens.

系统动力学曲线(Grenfell et al. 2004 Science 303, 327-332 (doi:10.1126/ Science .1090727))概念化了免疫如何通过其对病毒丰度和选择强度的相反作用,以非单调的方式塑造病毒适应的速度。然而,具体和定量的模型实现这一有影响的概念是罕见的。在这里,我们提出了一个分析性的随机框架,其中种群尺度的系统动力学曲线动态出现,使我们能够解决有关病毒免疫逃逸变异出现的风险和时间的问题。我们探讨了病原体和人群特异性参数(如免疫强度、传播性、季节性和抗原约束)如何影响出现风险。对于表现出明显季节性的病原体,我们发现可能的免疫逃逸变异出现的时间取决于地区之间病例输入的水平。受COVID-19大流行的影响,我们探讨了非药物干预措施(npi)及其解除对病毒逃逸变异出现风险的可能影响。展望未来,该框架有可能成为一种有用的工具,用于探索自然免疫、疫苗设计和分发中的选择以及国家行动计划的实施如何影响常见病毒病原体的进化。
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来源期刊
Journal of The Royal Society Interface
Journal of The Royal Society Interface 综合性期刊-综合性期刊
CiteScore
7.10
自引率
2.60%
发文量
234
审稿时长
2.5 months
期刊介绍: J. R. Soc. Interface welcomes articles of high quality research at the interface of the physical and life sciences. It provides a high-quality forum to publish rapidly and interact across this boundary in two main ways: J. R. Soc. Interface publishes research applying chemistry, engineering, materials science, mathematics and physics to the biological and medical sciences; it also highlights discoveries in the life sciences of relevance to the physical sciences. Both sides of the interface are considered equally and it is one of the only journals to cover this exciting new territory. J. R. Soc. Interface welcomes contributions on a diverse range of topics, including but not limited to; biocomplexity, bioengineering, bioinformatics, biomaterials, biomechanics, bionanoscience, biophysics, chemical biology, computer science (as applied to the life sciences), medical physics, synthetic biology, systems biology, theoretical biology and tissue engineering.
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