Blue Tongue Virus
Genome
The Blue Tongue Virus is an Orbivirus with a segmented double stranded RNA genome, containing 10 segments of sizes from 0.8kb to 4kb. It is the same family & genus of virus as the African Horse Sickness Virus. See http://viralzone.expasy.org/all_by_species/106.html
Subtypes
The main antigenic surface protein is VP2 (segment 2), and this is used to determine BTV subtype. There are 27 subtypes of BTV currently described (Feb 2017).
Figure 1: Number of VP2 sequences (Feb 2017) (Click to zoom)
|
VP2 Subtypes per host |
VP2 Subtypes per world region |
|
|
Sequences
VP2
VP2 sequences of each of the 24 serotypes from a study by Maan 2007:
Maan et al (2007) "Analysis and phylogenetic comparisions of full-length VP2 genes of the 24 bluetongue virus serotypes"
J Gen Virol 88:621-630
doi: 10.1099/vir.0.82456-0
| Segment | Protein | Sequences | NJ Tree | ML Tree |
| 2 | VP2 | 24 VP2 seqs | TN93 NJ Tree | GTR ML Tree with 100 bootstraps |
Figure 1: Maximum Likelihood tree of 24 Serotypes of VP2.
Click to zoom
Segments
Sequences from all segments were downloaded from GenBank on 19th May 2014. Initial processing to split the sequences into separate files according to segment was performed using a custom R script epic_process_background_seqs_blue_tongue.R, followed by manual editting of the sequence files.
Nucleotide sequences (fasta format) were initially aligned using Clustal, and then manually inspected and translated to amino acids for alignment using MUSCLE in MEGA 5.
Neighbour joining trees (newick format) were created in MEGA with the TN93 model, pairwise deletetion, and heterogenous rates between sites and lineages.
Table 1: Individual segments with GenBank accession numbers as names
| Segment | Length | Protein | Location | FASTA | Num.Seqs. | NJ Tree |
| L1 | 3909 | VP1 | core | segment 1 | 98 | NJ Tree |
| L2 | 3006 | VP2 | outer shell | segment 2 with 24 refs | 283+24 | NJ Tree |
| L3 | 2706 | VP3 | core | segment 3 | 149 | NJ Tree |
| M4 | 1938 | VP4 | core | segment 4 | 110 | NJ Tree |
| M5 | 1659 | NS1 | non-structural | segment 5 | 159 | NJ Tree |
| M6 | 1596 | VP5 | outer shell | segment 6 | 230 | NJ Tree |
| S7 | 1179 | VP7 | core | segment 7 | 56 | NJ Tree |
| S8 | 1050 | NS2 | non-structural | segment 8 | 198 | NJ Tree |
| S9 | 1067 | VP6 | core | segment 9 | 187 | NJ Tree |
| S10 | 803 | NS3/3A | non-structural | segment 10 | 358 | NJ Tree |
Reassortment
163 full genome sequences from a reassortment study by Nomikou et al (2015), with subtypes BTV-1 to BTV-25:
Nomikou et al (2015) "Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion"
PLoS Pathog 11(8):e1005056.
doi:10.1371/journal.ppat.1005056
Table 2: 163 full genomes from Nomikou 2015 study, aligned coding sequences
| Segment | Length | Protein | Location | FASTA | Num.Seqs. | Info |
| L1 | 3909 | VP1 | core | segment 1 | 163 | info |
| L2 | 2967 | VP2 | outer shell | segment 2 | 163 | info |
| L3 | 2706 | VP3 | core | segment 3 | 163 | info |
| M4 | 1935 | VP4 | core | segment 4 | 163 | info |
| M5 | 1659 | NS1 | non-structural | segment 5 | 163 | info |
| M6 | 1584 | VP5 | outer shell | segment 6 | 163 | info |
| S7 | 1050 | VP7 | core | segment 7 | 163 | info |
| S8 | 1065 | NS2 | non-structural | segment 8 | 163 | info |
| S9 | 993 | VP6 | core | segment 9 | 163 | info |
| S10 | 690 | NS3/3A | non-structural | segment 10 | 163 | info |
