Recent disease outbreaks have raised awareness of tropical pathogens, especially mosquito‐borne viruses. Dengue virus (DENV) is a widely studied mammalian pathogen transmitted by various species of mosquito in the genus Aedes, especially Aedes aegypti and Aedes albopictus. The prevailing view of the research community is that endemic viral lineages that cause epidemics of DENV in humans have emerged over time from sylvatic viral lineages, which persist in wild, non‐human primates. These notions have been examined by researchers through phylogenetic analyses of the envelope gene (E) from the four serotypes of DENV (serotypes DENV‐1 to DENV‐4). In these previous reports, researchers used visual inspection of a phylogeny in order to assert that sylvatic lineages lead to endemic clades. In making this assertion, these researchers also reasserted the model of periodic sylvatic to endemic disease outbreaks. Since that study, there has been a significant increase in data both in terms of metadata (e.g., place and host of isolation) and genetic sequences of DENV. Here, we re‐examine the model of sylvatic to endemic shifts in viral lineages through a phylogenetic tree search and character evolution study of metadata on the tree. We built a dataset of nucleotide sequences for 188 isolates of DENV that have metadata on sylvatic or endemic sampling along with three orthologous sequences from West Nile virus as the outgroup for the phylogenetic analysis. In contrast to previous research, we find that there are several shifts from endemic to sylvatic lineages as well as sylvatic to endemic lineages, indicating a much more dynamic model of evolution. We propose that a model that allows oscillation between sylvatic and endemic hosts better captures the dynamics of DENV transmission.

中文翻译：

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登革热病毒地方性和森林谱系的进化

最近的疾病暴发提高了人们对热带病原体，尤其是蚊媒病毒的认识。登革热病毒 (DENV) 是一种广泛研究的哺乳动物病原体，由伊蚊属的各种蚊子传播，尤其是埃及伊蚊和白纹伊蚊。研究界的普遍观点是，随着时间的推移，导致人类 DENV 流行的地方性病毒谱系已经从森林病毒谱系中出现，这种病毒谱系在野生、非人类灵长类动物中持续存在。研究人员通过对来自四种 DENV 血清型（血清型 DENV-1 至 DENV-4）的包膜基因 (E) 的系统发育分析来检验这些概念。在之前的这些报告中，研究人员使用系统发育的目视检查来断言森林谱系导致地方性进化枝。在做出这个断言时，这些研究人员还重申了周期性到地方病爆发的模型。自那项研究以来，在元数据（例如，隔离的地点和宿主）和 DENV 的基因序列方面的数据都显着增加。在这里，我们通过系统发育树搜索和树元数据的特征进化研究，重新检查了病毒谱系从森林到地方性转变的模型。我们为 188 个 DENV 分离株建立了一个核苷酸序列数据集，这些分离株具有森林或地方性采样的元数据，以及来自西尼罗河病毒的三个直系同源序列作为系统发育分析的外群。与之前的研究相比，我们发现从地方性到森林世系以及森林到地方性世系有几种转变，表明进化的动态模型要多得多。