Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modelling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centres in the Southeast. Phylodynamic analysis unravelled the circulation of three distinct YFV lineages, and provided proof of the directionality of a known spatial corridor of viral spread that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology in a One Health framework can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

尽管巴西境内的黄热病毒（Yellow Fever Virus, YFV）感染可造成较高的发病率与死亡率，但学界对该病暴发的认知仍受限于病毒基因组数据的匮乏。明确黄热病毒的传播时间与空间廊道，以及连接该国地方性流行北部地区与亚马逊以外流行区域的地理热点，是预测并防范未来暴发与疫情的核心所在。
本研究通过整合基因组序列、流行病学数据与媒介数据，追踪了该病毒近期的传播态势。结合系统发育模型与流行病学模型，本研究还原了巴西不同疫情季内黄热病毒的近期传播历程。基于高度家养型埃及伊蚊（Aedes aegypti）构建的适宜性指数，能够反映报告的人类感染病例的季节特征。空间建模结果显示，既往存在病例报告且疫苗接种覆盖率较低的地理热点区域，与巴西东南部多数大型城市中心高度吻合。系统发育动力学分析揭示了3个不同的黄热病毒谱系的循环传播特征，并证实了一条已知病毒传播空间廊道的方向性——该廊道连接地方性流行的北部地区与亚马逊河以外流域。
本研究表明，在同一健康（One Health）框架下结合基因组学与生态流行病学，能够为解析黄热病毒的传播全景格局提供新视角，补充传统传染病监测与防控手段。