Full-Genome Characterisation of Orungo, Lebombo and Changuinola Viruses Provides Evidence for Co-Evolution of Orbiviruses with Their Arthropod Vectors

Abstract

The complete genomes of Orungo virus (ORUV), Lebombo virus (LEBV) and Changuinola virus (CGLV) were sequenced, confirming that they each encode 11 distinct proteins (VP1-VP7 and NS1-NS4). Phylogenetic analyses of cell-attachment protein ‘outer-capsid protein 1′ (OC1), show that orbiviruses fall into three large groups, identified as: VP2(OC1), in which OC1 is the 2nd largest protein, including the Culicoides transmitted orbiviruses; VP3(OC1), which includes the mosquito transmitted orbiviruses; and VP4(OC1) which includes the tick transmitted viruses. Differences in the size of OC1 between these groups, places the T2 ‘subcore-shell protein’ as the third largest protein ‘VP3(T2)’ in the first of these groups, but the second largest protein ‘VP3(T2)’ in the other two groups. ORUV, LEBV and CGLV all group with the Culicoides-borne VP2(OC1)/VP3(T2) viruses. The G+C content of the ORUV, LEBV and CGLV genomes is also similar to that of the Culicoides-borne, rather than the mosquito-borne, or tick borne orbiviruses. These data suggest that ORUV and LEBV are Culicoides- rather than mosquito-borne. Multiple isolations of CGLV from sand flies suggest that they are its primary vector. OC1 of the insect-borne orbiviruses is approximately twice the size of the equivalent protein of the tick borne viruses. Together with internal sequence similarities, this suggests its origin by duplication (concatermerisation) of a smaller OC1 from an ancestral tick-borne orbivirus. Phylogenetic comparisons showing linear relationships between the dates of evolutionary-separation of their vector species, and genetic-distances between tick-, mosquito- or Culicoides-borne virus-groups, provide evidence for co-evolution of the orbiviruses with their arthropod vectors.

Letea Virus: Comparative Genomics and Phylogenetic Analysis of a Novel Reassortant Orbivirus Discovered in Grass Snakes (Natrix natrix)

“…The NS4 is a nonstructural protein found in some orbiviruses and the last one described to date [41,42]. In LEAV, we found NS4 to be of similar size and position as in other C/SBOV [9,41,43], showing also the lowest sequence identity among all compared orbiviral proteins ( Table 2).…”

“…The LEAV terminal nucleotides are not conserved hexanucleotides as in the case of BTV or AHSV, but heptanucleotides showing little variation among the 10 segments. Distal dinucleotides at both of the UTR ends are inverted complements (Table 1), as shown in other orbiviruses [1,3,6,9,[38][39][40].…”

“…Previous studies noted that the overall GC content and the UTR proportion relative to the genome's length reflect three groups similar to those illustrated by phylogenetic analyses. First, the GC content is highest in TBOV with 52-57.3% GC, followed by the C/SBOV with 39.9-45.9% GC and the MBOV with 36.7-41.6% GC [6,9,39,43]. The GC content of LEAV is 34.6-34.9%, therefore below these intervals.…”

“…The phylogenetic trees based on VP1 and T13 amino acid (Figure 2a,b) and nucleotide sequences ( Figure S1) displayed a clustering typical for the Orbivirus genus, with main clades indicative of their arthropod vectors [9]. The three main branches are rooted by SCRV, an orbivirus isolated from tick cells which is considered a tick-associated orbivirus (TOV) [5].…”

“…In contrast, the proteins of the outer capsid are highly variable and their specificity to the host's neutralizing antibody response can be used to distinguish between different serotypes of the same orbivirus species [7,8]. The phylogenetic clustering of Orbivirus members results in clades indicating their putative or potential arthropod vectors: Culicoidesor sand fly-borne (C/SBOV), mosquito-borne (MBOV) and tick-borne orbiviruses (TBOV) [9]. One exception to this classification is St. Croix River virus (SCRV), a distant member of the genus considered to be a "tick orbivirus" (TOV), having no known vector [5].…”