Blue Tongue Virus


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


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



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

SegmentProteinSequencesNJ TreeML Tree
2VP2 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


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
SegmentLengthProteinLocationFASTANum.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


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
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