英国剑桥大学Noémie Lefrancq团队近期取得重要工作进展，他们从系统发育学的角度学习分析了病原体的适应度动态。相关研究成果2025年1月1日在线发表于《自然》杂志上。

据介绍，病原体遗传多样性的动态，包括适应性增强谱系的出现，是具有关键公共卫生影响的疾病生态学的基本概念。然而，这种谱系的识别和相关适应度的估计仍然具有挑战性，很少在密集采样系统之外进行。

研究人员提出了phylowave，这是一种可扩展的方法，可以总结系统发育树中种群组成的变化，从而能够基于共享的适应度和演化关系自动检测谱系。研究人员对一系列广泛的病毒和细菌（严重急性呼吸系统综合征冠状病毒2型、甲型流感H3N2亚型、百日咳杆菌和结核分枝杆菌）使用这一方法，其中包括对人类健康的威胁进行了充分研究和研究不足。研究人员表明，phylowave可以恢复每种病原体的主要已知循环谱系，并且可以检测与适应度变化相关的特定氨基酸变化。

此外，phylowave识别出以前未被发现的适应性增强的谱系，包括三个共循环的百日咳杆菌谱系。这种广泛适用的方法提供了一种实时监测演化的途径，以支持公共卫生行动并探索病原体适应性的基本驱动因素。

附：英文原文

Title: Learning the fitness dynamics of pathogens from phylogenies

Author: Lefrancq, Nomie, Duret, Lorna, Bouchez, Valrie, Brisse, Sylvain, Parkhill, Julian, Salje, Henrik

Issue&Volume: 2025-01-01

Abstract: The dynamics of the genetic diversity of pathogens, including the emergence of lineages with increased fitness, is a foundational concept of disease ecology with key public-health implications. However, the identification of such lineages and estimation of associated fitness remain challenging, and is rarely done outside densely sampled systems1,2. Here we present phylowave, a scalable approach that summarizes changes in population composition in phylogenetic trees, enabling the automatic detection of lineages based on shared fitness and evolutionary relationships. We use our approach on a broad set of viruses and bacteria (SARS-CoV-2, influenza A subtype H3N2, Bordetella pertussis and Mycobacterium tuberculosis), which include both well-studied and understudied threats to human health. We show that phylowave recovers the main known circulating lineages for each pathogen and that it can detect specific amino acid changes linked to fitness changes. Furthermore, phylowave identifies previously undetected lineages with increased fitness, including three co-circulating B.pertussis lineages. Inference using phylowave is robust to uneven and limited observations. This widely applicable approach provides an avenue to monitor evolution in real time to support public-health action and explore fundamental drivers of pathogen fitness.

DOI: 10.1038/s41586-024-08309-9

Source: https://www.nature.com/articles/s41586-024-08309-9