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

Abstract

A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.

Fig. 1.

Phylogenetic tree of members of the genus Orthobunyavirus based on the protein-coding portion of the L segment. The tree was built using translated amino acid sequences in mega v5.1 (Tamura et al., 2011) using the neighbour-joining algorithm and a p-distance matrix. The tree is unrooted and the node labels represent percentage bootstrap support values after 1000 resampling events. Filled circles indicate the genomes that were sequenced in this study. Species designations (left brackets) are based on the genetic data presented in this paper. Clade labels on the far right correspond to serogroups.

Fig. 2.

Pairwise genetic similarities (1−amino acid p-distance) among viruses within and between serogroups of orthobunyaviruses based on the L segment (a) and S segment (b). For the two Simbu serogroup clades, an extra category is presented that includes only the pairwise similarities between these two groups; this is a subset of the intergroup distances for both clade A and clade B. See Tables S2 and S3 for the list of sequences used in these analyses.

Fig. 3.

Nucleotide-level phylogenetic trees including only the fully sequenced members of the Oropouche and Manzanilla species complexes. All trees were built in mega v5.1 (Tamura et al., 2011) using the maximum-likelihood framework with partial deletions. The trees are unrooted. Node labels represent percentage bootstrap support values after 1000 resampling events.