Evolutionary Dynamics of Oropouche Virus in South America

Abstract

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 Peribunyaviridae, 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.

Characterising West Nile virus epidemiology in Israel using a transmission suitability index

“…Important examples of these trends are the recent Zika virus epidemic, which had severe public health consequences in Central and South America [5][6][7][8], the yellow fever vaccination crisis in African countries [9] and (re)emergence of yellow fever virus in Brazil [9,10]. Other examples of mosquito-borne viruses experiencing recent surges include chikungunya, Mayaro, Usutu, Spondweni, Oropuche and West Nile viruses [1,3,11].…”

Oropouche virus cases identified in Ecuador using an optimised qRT-PCR informed by metagenomic sequencing

“…The group is most closely related to strain TVP-19256/IQE-7894 from Peru, 2008 (GenBank KP795084.1-KP795086.1). A comprehensive phylogenetic analysis of OROV in South America, including the Ecuadorian genomes, has been undertaken [26].…”

“…Primer and probe sequences were aligned using the ClustalW algorithm in the MEGA7 software package, to a set of OROV N gene coding sequences (GenBank) representing the geographic (Brazil, Panama, Peru and Trinidad and Tobago) and temporal diversity of OROV isolates from the 1950s to present day [26].…”

Common Dysregulation of Innate Immunity Pathways in Human Primary Astrocytes Infected With Chikungunya, Mayaro, Oropouche, and Zika Viruses

“…Tropical countries of South America, such as Brazil, are specially in risk for arboviruses outbreaks due to the suitable warm weather, abundance of insect vectors, deforestation, high population concentration near forest areas, social-economical disparities, and overburden of the public healthcare system ( Peña-García et al., 2017 ; Figueiredo, 2019 ; Medeiros and Vasconcelos, 2019 ). Many endemic outbreaks along the history, as well the recent introduction of arboviruses in Brazil, have risen the alarm of scientific and medical communities concerning the risk of new outbreaks, co-circulation of those viruses, and increasing of more severe cases ( Metsky et al., 2017 ; Zanotto and Leite, 2018 ; Lorenz et al., 2019 ; Gutierrez et al., 2020 ). Viruses members of Alphavirus , Orthobunyavirus , and Flavivirus genus ( Togaviridae , Peribunyaviridae , and Flaviviridae viral families, respectively) present a higher incidence in Brazil and has been associated to a plethora of clinically relevant outcomes, such as mild to debilitating fever, hemorrhagic fever, arthritis, microcephaly, and neurological disorders ( Figueiredo, 2015 ; Santiago et al., 2015 ; Burt et al., 2017 ; Azeredo et al., 2018 ; Vernal et al., 2019 ; Brito Ferreira et al., 2020 ; Diagne et al., 2020 ; Gutierrez et al., 2020 ).…”