Genomic and phylogenetic characterization of viruses included in the Manzanilla 1 and Oropouche species complexes of the genus Orthobunyavirus , family

and Oropouche species complexes of the genus Orthobunyavirus, family 2 Bunyaviridae 3 4 Summary 33 A thorough characterization of the genetic diversity of viruses present in vector 34 and vertebrate host populations is essential for the early detection of and response to 35 emerging pathogenic viruses, yet genetic characterization of many important viral groups 36 remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family 37 Bunyaviridae is an example. The Simbu serogroup currently consists of a highly diverse 38 group of related arboviruses that infect both humans and economically important 39 livestock species. Here, we report complete genome sequences for 11 viruses within this 40 group, with a focus on the large and poorly characterized Manzanilla and Oropouche 41 species complexes. Phylogenetic and pairwise divergence analyses indicate the presence 42 of high-levels of genetic diversity within these two species complexes, on par with that 43 seen among the five other species complexes in the Simbu serogroup. Based on 44 previously reported divergence thresholds between species, the data suggest that these 45 two complexes should actually be divided into at least five species. Together these five 46 species form a distinct phylogenetic clade apart from the rest of the Simbu serogroup. 47 Pairwise sequence divergences among viruses of this clade and viruses in other Simbu 48 serogroup species complexes are similar to levels of divergence among the other 49 orthobunyavirus serogroups. The genetic data also suggest relatively high levels of 50 natural reassortment, with three potential reassortment events present, including two 51 well-supported events involving viruses known to infect humans. 52 4 Introduction 53