Contents lists available at ScienceDirect Infection, Genetics and Evolution journal homepage: www.elsevier.com/locate/meegid Research paper Oropouche orthobunyavirus: Genetic characterization of full-length genomes and development of molecular methods to discriminate natural reassortments Márcio Roberto Teixeira Nunes a,b, ⁎ ,1 , William Marciel de Souza c,d,1 , Nazir Savji e , Mário Luís Figueiredo f , Jedson Ferreira Cardoso a,g , Sandro Patroca da Silva h , Clayton Pereira da Silva de Lima a , Helena Baldez Vasconcelos h , Sueli Guerreiro Rodrigues h , W. Ian Lipkin i,1 , Pedro Fernando Costa Vasconcelos h,1 , Gustavo Palacios j,1 a Center for Technological Innovations, Evandro Chagas Institute, Ministry of Health, Ananindeua, Pará, Brazil b Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA c Virology Research Center, School of Medicine of Ribeirao Preto of University of São Paulo, Ribeirao Preto, São Paulo, Brazil d MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, United Kingdom e Department of Medicine, Massachusetts General Hospital, Boston, MA, USA f Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil g Posgraduate Program in Virology, Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil h Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, Brazil i Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, New York, USA j The Center for Genome Science, US Army Medical Research Institute of Infectious Disease at Fort Detrick, MD, USA ARTICLE INFO Keywords: Oropouche orthobunyavirus Peribunyaviridae Viral genotyping Molecular diagnosis Arbovirus ABSTRACT Oropouche orthobunyavirus (OROV) has significant impact in public health in Amazon region. This arbovirus is one of the most common causes of febrile illness in Brazil, and is responsible for several epidemics since 1960's. In this study, we sequenced and characterized the complete coding sequences (S-, M- and L-RNA) of 35 OROV isolates from Brazil. Here, we classified 20 strains in genotype I from Pará and Maranhão states, nine as genotype II from Pará and Rondônia states confirmed, four classified into genotype III from Acre, Maranhão, Minas Gerais and Rondônia states and two genotype IV from Amazonas State. Also, we did not observe reassortment events involving the OROV isolates. In addition, we developed novel RT-PCR tools to identify reassortment events among OROV strains. These data will be useful to better understand the molecular epidemiology and diagnostic of OROV infections. 1. Introduction Oropouche orthobunyavirus (OROV) is one of the most important arboviruses in the Amazon region. This virus is classified into Simbu serogroup, genus Orthobunyavirus, Peribunyaviridae family (Travassos Da Rosa et al., 2017). The prototype of OROV was isolated from a febrile patient in the rural village of Vega de Oropouche in 1955, Tri- nidad and Tobago (Anderson et al., 1961). In Brazil, this virus was first isolated in 1960 from the blood of a sloth (Bradypus trydactylus) cap- tured during the construction of the Belém-Brasília Highway. In the last 60 years, > 30 outbreaks have been caused by OROV in Latin America, where approximately half million people have been infected (Travassos Da Rosa et al., 2017). In the last decade, improvements in genome sequencing methods allowed several OROV strains to be completely or partially sequenced. Consequently, new insights into evolutionary history, epidemiology, reassortment events, and genotype classification of OROV species have been unearthed (Aguilar et al., 2011; Hontz et al., 2015; Navarro et al., 2016; Saeed et al., 2000; Tilston-Lunel et al., 2015b; Vasconcelos et al., 2011). However, the majority of studies have been limited to sequen- cing the S segment (Bastos et al., 2014; Cardoso et al., 2015; de Souza Luna et al., 2017; Gibrail et al., 2016). Viral taxonomy and evolutionary analysis are improved by the inclusion of multiple genetically distinct genomes, thereby ensuring a range of genetic diversity in phylogenetic https://doi.org/10.1016/j.meegid.2018.11.020 Received 28 February 2018; Received in revised form 20 October 2018; Accepted 28 November 2018 ⁎ Corresponding author at: Center for Technological Innovation, Instituto Evandro Chagas, Ananindeua, Brazil. E-mail address: marcionunes@iec.pa.gov.br (M.R.T. Nunes). 1 These authors have contributed equally to this study. Infection, Genetics and Evolution 68 (2019) 16–22 Available online 29 November 2018 1567-1348/ © 2018 Published by Elsevier B.V. T