When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical, and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats.

中文翻译：

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跨尺度动力学和传染病的进化出现


当新出现的病原体遇到它们不适应的新宿主物种时，它们必须进化才能避免灭绝。病原体在多个尺度上经历性状选择，包括宿主个体内的复制率和宿主之间的传播性。我们分析了一个随机模型，将病原体的生长和个体内部的竞争与个体之间的传播联系起来。我们的分析揭示了一个新因素，即突变病毒颗粒的跨尺度繁殖数，它可以量化突变菌株最初出现在受感染宿主群体中时频率增加的速度。这种跨尺度的繁殖数与病毒突变率、单株繁殖数和传播瓶颈宽度相结合，以确定进化出现的可能性，以及进化在传播链内是迅速发生还是逐渐发生。我们发现，更广泛的传播瓶颈促进了具有短期感染的病原体的出现，但阻碍了表现出跨尺度选择性冲突和长期感染的病原体的出现。我们的研究结果提供了一个框架，可以在进化理论的背景下推进实验室、临床和现场数据的整合，为新一代基于证据的突发威胁风险评估奠定基础。