Table 1.
Accession numbers of sequences downloaded from databases.
Table 2.
Lengths of dsRNA segments, encoded putative proteins, 5' and 3' non coding regions (NCR) and G+C content of ORUV, LEBV and CGLV.
Table 3.
Correspondence between Orungo virus (ORUV), Lebombo virus (LEBV), and Changuinola virus (CGLV).
Table 4.
Correspondence between Orungo virus (ORUV) and Great Island virus (GIV: a tick-borne orbivirus), Bluetongue virus (BTV: a typical Culicoides-borne orbivirus), St Croix River virus (SCRV: a tick-borne orbivirus belonging to a distinct species) and Yunnan orbivirus (YUOV) a mosquito-borne orbivirus.
Table 5.
Correspondence between Lebombo virus (LEBV) and Great Island virus (GIV: a tick-borne orbivirus), Bluetongue virus (BTV: a typical Culicoides-borne orbivirus), St Croix River virus (SCRV: a tick-borne orbivirus belonging to a distinct species) and Yunnan orbivirus (YUOV) a mosquito-borne orbivirus.
Table 6.
Correspondence between Changuinola virus (CGLV) and Great Island virus (GIV: a tick-borne orbivirus), Bluetongue virus (BTV: a typical Culicoides-borne orbivirus), St Croix River virus (SCRV: a tick-borne orbivirus belonging to a distinct species) and Yunnan orbivirus (YUOV) a mosquito-borne orbivirus.
Table 7.
Sequences of ORUV, LEBV or CGLV NLS’s.
Figure 1.
Maximum likelihood trees showing phylogenetic comparisons of the aa sequences of VP1 of ORUV, LEBV and CGLV, aligned with those of other Orbivirus species.
Figure 1 is an ML amino acid tree, respectively, both depicting the three groups of orbiviruses (i-Culicoides−/sandfly-borne, ii- mosquito-borne and iii- tick-borne) as separate clusters. The polymerase of Banna virus (genus Seadornavirus, family Reoviridae: a 12-segmented mosquito-borne dsRNA virus) used as outgroup. This figure shows the root to be located between the tick/tick-borne orbiviruses and the insect-borne orbiviruses. LEBV, ORUV and CGLV all cluster among Culicoides-borne orbiviruses. The scale bar represents the number of substitutions per site.
Figure 2.
A neighbour joining tree showing phylogenetic comparisons the aa sequences of T2 (VP2(T2) of mosquito-borne and tick-borne orbiviruses and VP3(T2) of Culicoides-borne orbiviruses) aligned with those of ORUV, LEBV and CGLV.
The tree depicts the groups of Culicoides-borne and sandfly-borne viruses having their VP3 as the T2 protein, while the tick-borne and mosquito-borne viruses having their VP2 as the T2 protein. LEBV, ORUV and CGLV all cluster among Culicoides-borne orbiviruses. The scale bar represents the number of substitutions per site.
Figure 3.
Maximum likelihood trees showing phylogenetic comparisons of the amino acid of cytochrome oxidase I (COXI) of arthropods.
ML tree of COXI of 3 groups of arthropods which transmit orbiviruses (ticks, mosquitoes and Culicoids). The scale bar represents the number of substitutions per site.
Figure 4.
Maximum likelihood trees showing phylogenetic comparisons of the amino acid of antigen 5-related proteins of arthropods.
ML tree of the antigen 5-related proteins of all 4 groups of arthropods (ticks, mosquitoes, Culicoids and sandflies) depicting Culicoides and sandflies as one cluster. The scale bar represents the number of substitutions per site.
Figure 5.
Comparison of topologies of orbivirus VP1(Pol) tree in (i) to vector COXI proteins in (ii).
Comparison of topologies of orbivirus VP1(Pol) tree in (i) to that of vector COXI (Culicoides, mosquitoes and ticks) in (ii). The topologies of the vector proteins based trees mirror those of the VP1(Pol) trees of orbiviruses. The scale bar represents the number of substitutions per site.
Figure 6.
Comparison of topologies of orbivirus VP1(Pol) tree in (i) to vector antigen 5-related proteins in (ii).
Comparison of topologies of orbivirus VP1(Pol) tree in (i) to that of vector antigen 5-related proteins (Culicoides, sandflies, mosquitoes and ticks) in (ii). The topologies of the vector proteins based trees mirror those of the VP1(Pol) trees of orbiviruses. The scale bar represents the number of substitutions per site.
Figure 7.
Maximum likelihood trees showing phylogenetic comparisons of the nucleotide sequences of the genome segment encoding the VP7(T13) proteins of ORUV, LEBV and CGLV, aligned with those of other Orbivirus species.
The nucleic acid sequences were aligned based on the profile of aa alignments generating a codon to codon alignment, showing the three groups of orbiviruses (i-Culicoides−/sandfly-borne, ii- mosquito-borne and iii- tick-borne) as separate clusters. LEBV, ORUV and CGLV all cluster among Culicoides-borne orbiviruses. The scale bar represents the number of substitutions per site.
Table 8.
Genetic distances between the most divergent viruses among tick-borne, mosquito-borne or Culicoides-borne orbiviruses.
Figure 8.
Linear relationships linking the largest genetic distances between tick-borne, mosquito-borne or Culicoides-borne orbiviruses and time of divergence for vectors.
The largest genetic distance within a group of orbiviruses (tick-borne, mosquito-borne or Culicoides-borne) is plotted against the date of separation of vector groups (ticks, mosquitoes or midges). A linear relationship is depicted for both the VP1(Pol) and the T2 (correlation coefficient R2>0.99), and is less obvious in the T13 protein (R2 = 0.9311).
Figure 9.
Electropherotypes of a tick-borne (GIV), mosquito-borne (YOUV) and Culicoides-borne (BTV) orbivirus and relatedness of the GIV VP4 to BTV VP2. A:
Electropherotypes of Great Island virus (GIV), Yunnan orbivirus (YUOV) and Bluetongue virus (BTV) showing the genome segments encoding OC1 and OC2 in tick-, mosquito and Culicoides-borne orbiviruses. B: a schematic of the match between the VP4(OC1) of GIV and VP2(OC1) of BTV. VP4 (OC1) of tick-borne orbiviruses is 55% the length of VP2(OC1) of Culicoides-borne or VP3(OC1) of mosquito-borne orbiviruses. Amino acids 45–501 of VP4 matches the COOH terminal half of OC1s of insect-borne orbiviruses (e.g: VP2(OC1) of BTV: aa 520–901). C: Hydrophobicity profiles of GIV VP4 and domain 2 of BTV VP2 (VP2D2); the two profiles are broadly similar and show the plot of aa 114 to 523 of VP4 (blue line) superimposed onto that of aa 642 to 956 of VP2D2 (red line).
Figure 10.
Neighbour-joining Amino acid tree depicting the three groups of tick-borne, mosquito-borne and Culicoides-borne OC1.
The topology of orbivirus OC1-based tree is similar to that of the T2 protein and the VP7 coding nucleotide sequence-based trees. LEBV, ORUV and CGLV all cluster among Culicoides-borne orbiviruses. The scale bar represents the number of substitutions per site.
Figure 11.
Potential duplications in BTV VP2(OC1).
OC1 sequence of BTV VP2 with repeats identified by REPRO. The sequences in blue font represent the NH2 terminal domain while the sequences in the red font represent the COOH terminal domain. Superimposed hydrophobicity profiles of the two domains are shown below each alignment. The amino acid identity between the two identified repeats is 29%. Hydrophobicity profiles of repeats are shown below the alignment. In BTV VP2, aa 63 to 471 were identified as a repeat of aa 500 to 955. Finer sequence analyses identified that aa75–442 have highly similar hydrophobicity plots to aa 567–955.
Figure 12.
Potential duplications in YUOV VP3(OC1).
OC1 sequence of YUOV VP3 with repeats identified by REPRO. The sequences in blue font represent the NH2 terminal domain while the sequences in the red font represent the COOH terminal domain. Superimposed hydrophobicity profiles of the two domains are shown below each alignment. The amino acid identity between the two identified repeats is 28%. Hydrophobicity profiles of repeats are shown below the alignment. In YUOV VP3, aa 11 to 448 were identified as a repeat of aa 45 to 851. Finer sequence analysis identified that aa 60–448 have highly similar hydrophobicity plots to aa 462–851.
Figure 13.
Potential duplications in ORUV VP2(OC1).
OC1 sequence of ORUV VP2 with repeats identified by REPRO. The sequences in blue font represent the NH2 terminal domain while the sequences in the red font represent the COOH terminal domain. Superimposed hydrophobicity profiles of the two domains are shown below each alignment. The amino acid identity between the two identified repeats is 31%. Hydrophobicity profiles of repeats are shown below the alignment. In ORUV VP2, aa 26 to 421 were identified as a repeat of aa 427 and 899 of the same protein. Finer sequence analysis identified that aa 75–384 have highly similar hydrophobicity plots to aa 520–899.
Figure 14.
Potential duplications in SCRV VP3(OC1).
OC1 sequence of SCRV VP3 with repeats identified by REPRO. The sequences in blue font represent the NH2 terminal domain while the sequences in the red font represent the COOH terminal domain. Superimposed hydrophobicity profiles of the two domains are shown below each alignment. The amino acid identity between the two identified repeats is 28%. In SCRV VP3, aa 1 to 81 of SCRV may also represent a duplication of aa 88 to 160. Hydrophobicity profiles of repeats are shown below the alignment. The hydrophobicity plots of the two sequences in SCRV VP3 are similar.