Damodaran Lambodhar, de Bernardi Schneider Adriano, Chen Shi, Janies Daniel
Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, 28223-0001, NC, USA.
Institute of Bioinformatics, University of Georgia, 120 Green St., Athens, 30602, GA, USA.
Cladistics. 2020 Apr;36(2):115-128. doi: 10.1111/cla.12402. Epub 2019 Sep 19.
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.
近期的疾病爆发提高了人们对热带病原体的认识，尤其是蚊媒病毒。登革病毒（DENV）是一种经过广泛研究的哺乳动物病原体，由伊蚊属的多种蚊子传播，特别是埃及伊蚊和白纹伊蚊。研究界的普遍观点是，导致人类登革热流行的地方性病毒谱系是随着时间的推移从存在于野生非人类灵长类动物中的丛林病毒谱系演变而来的。研究人员通过对登革病毒四种血清型（血清型DENV-1至DENV-4）的包膜基因（E）进行系统发育分析，对这些观点进行了研究。在这些先前的报告中，研究人员通过对系统发育树的目视检查来断言丛林谱系导致地方性分支。在提出这一断言时，这些研究人员还重申了周期性丛林到地方性疾病爆发的模型。自该研究以来，无论是在元数据（例如分离地点和宿主）方面还是在登革病毒的基因序列方面，数据都有了显著增加。在这里，我们通过系统发育树搜索和对树上元数据的特征进化研究，重新审视病毒谱系从丛林到地方性转变的模型。我们构建了一个包含188株登革病毒核苷酸序列的数据集，这些序列具有关于丛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。与先前的研究不同，我们发现有几个从地方性谱系到丛林谱系以及从丛林谱系到地方性谱系的转变，这表明进化模型更加动态。我们提出，一个允许在丛林宿主和地方性宿主之间振荡的模型能更好地捕捉登革病毒传播的动态。
