Evolutionary Dynamics of Oropouche Virus in South America
Evolutionary Dynamics of Oropouche Virus in South America
复制标题
DOI：
10.1128/jvi.01127-19
复制
发表时间：
2020-03-01
影响因子：
5.4
通讯作者：
Pybus, Oliver G.
中科院分区：
文献类型：
--
作者：
Gutierrez, Bernardo;Wise, Emma L.;Pybus, Oliver G.
亚马逊盆地是许多节肢动物传播的病毒性病原体的家园，这些病原体会导致人类发烧。其中，Oropouche orthobunyavirus （OROV）是原布尼亚病毒属（Peribuoyaviridae）的一种研究相对较少的成员，该病毒在巴西和其他南美国家的人群中引起周期性暴发。尽管有几项研究描述了该病毒的遗传多样性，但形成OROV基因组的进化过程仍然知之甚少。在此，我们对OROV的基因组动力学进行了全面的研究，包括系统发育分析、进化速率估计、自然选择压力推断、重组和重排以及OROV变异的结构分析。我们的研究包括所有可用的已发表的序列，以及从厄瓜多尔患者身上获得的一组新的OROV基因组序列，这是该国的第一组基因组。我们的研究结果显示了组成病毒基因组的三个片段的不同进化过程。我们推断基因组片段最近共同祖先的不同时间，并提出这可以通过隐式重组来解释。我们还发现了以前未观察到的假定的n链糖基化位点，以及在病毒表面蛋白的正选择下进化的密码子，并通过系统发育和结构的结合方法讨论了这些特征在OROV进化中的潜在作用。寨卡病毒、基孔肯雅病毒和黄热病病毒等病原体的出现和重新出现引起了人们对南美洲其他共流行虫媒病毒的关注。Oropouche病毒（OROV）是一种研究甚少的病原体，自20世纪60年代初以来曾造成十几次疫情，对巴西、巴拿马和秘鲁等国构成了公共卫生负担。由于其症状很容易与其他发热性疾病（如登革热和钩端螺旋体病）混淆，而且对该病毒的即时检测仍然不常见，因此OROV可能被低估了。由于数据有限，有必要优化当前可用的信息。对OROV基因组的分析可以帮助我们了解病毒在自然界中的传播方式，并可以揭示形成病毒遗传多样性的进化力量，这对分子诊断和潜在疫苗的设计具有重要意义。
The Amazon basin is home to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these, Oropouche orthobunyavirus (OROV) is a relatively understudied member of the genus Orthobunyavirus, family Peribuoyaviridae, that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the OROV genome remain poorly understood. Here, we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genome sequences obtained from patients in Ecuador, representing the first set of genomes from this country. Our results show differing evolutionary processes on the three segments that comprise the viral genome. We infer differing times of the most recent common ancestors of the genome segments and propose that this can be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, as well as codons that evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of OROV through a combined phylogenetic and structural approach.IMPORTANCE The emergence and reemergence of pathogens such as Zika virus, chikungunya virus, and yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche virus (OROV) is a poorly studied pathogen responsible for over a dozen outbreaks since the early 1960s and represents a public health burden to countries such as Brazil, Panama, and Peru. OROV is likely underreported since its symptomatology can be easily confounded with other febrile illnesses (e.g., dengue fever and leptospirosis) and point-of-care testing for the virus is still uncommon. With limited data, there is a need to optimize the information currently available. Analysis of OROV genomes can help us understand how the virus circulates in nature and can reveal the evolutionary forces that shape the genetic diversity of the virus, which has implications for molecular diagnostics and the design of potential vaccines.