Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses

Abstract

Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito-bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1, U2, and U3 that apparently arose by gene duplication. To further investigate the U1-U2-U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically.

Evolution of Genome Size and Complexity in the Rhabdoviridae

“…5). As previously observed for FLAV, this 'stop-start' arrangement is commonly preceded by a 'termination upstream ribosome-binding site' (TURBS), which contains a short sequence motif that is complementary to the loop region of helix 26 of 18S ribosomal RNA [19,41]. The TURBS may also contain flanking anti-complementary sequence motifs that are predicted to form a stem-loop structure.…”

“…Gene duplication. Previous studies have provided evidence of gene duplication in the Rhabdoviridae, involving the G and G NS genes [18,21] and the β and γ genes [22] in the ephemeroviruses, and the U1, U2 and U3 genes in the hapaviruses FLAV and WONV [15,19,20]. To identify further examples of gene duplication, we conducted a BLAST analysis of all proteins in our database (E-value <1e-3) and used ClustalX alignments to confirm sequence similarity.…”

“…4). Several of these proteins have been identified previously [19,22,[29][30][31][32][33][34][35]. Like the BEFV α1 protein for which viroporin activity has been confirmed experimentally, these proteins have the structure characteristics of class IA viroporins, including a central transmembrane and a highly basic C-terminal domain.…”

“…Rhabdovirus genomes may also contain additional ORFs encoding putative proteins, which are mostly of unknown function. These may occur as alternative or overlapping ORFs within the major structural protein genes or as independent ORFs flanked by TI or TTP sequences in the regions between the structural protein genes [15], some of which appear to have arisen by gene duplication [15,[18][19][20][21][22].…”

Taxonomy of the order Mononegavirales: update 2017

“…Twelve mostly dipteran viruses (Hart Park virus, Gray Lodge virus, Joinjakaka virus, Kamese virus, La Joya virus, Landjia virus, Manitoba virus, Marco virus, Mosqueiro virus, Mossuril virus, Ord River virus, and Parry Creek virus), isolated in the 1950s to late 1970s, were classified into twelve new species in the new genus Hapavirus . The previously free-floating rhabdovirus species Flanders virus , Ngaingan virus , and Wongabel virus were moved into the genus Hapavirus and renamed accordingly ( Flanders hapavirus , Ngaingan hapavirus , and Wongabel hapavirus , respectively) [4, 21, 44] (TaxoProp 2016.005a-gM.A.v4.Hapavirus). The largest newly created rhabdovirus genus is Ledantevirus .…”