African Horse Sickness Virus

Sequences

African Horse Sickness sequences were downloaded from GenBank on 25th Oct 2013.
Initial processing to split the sequences into separate files according to segment was performed using a custom R script epic_process_background_seqs_african_horse_sickness.R, followed by manual editting of the sequence files.

Nucleotide sequences (fasta format) were 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.

Segment and protein information from Roy et al 1994

All sequences with original full names as zip file

Table 1: Individual segments with original full names

Segment Length Protein Location FASTA Num.Seqs. NJ Tree

L1 3500 VP1 core segment 1 7 NJ Tree

L2 3229 VP2 outer shell segment 2 55 See individual serotype files

L3 2792 VP3 core segment 3 22 NJ Tree

M4 1978 VP4 core segment 4 21 NJ Tree

M5 1751 NS1 non-structural segment 5 63 NJ Tree

M6 1566 VP5 outer shell segment 6 32 NJ Tree

S7 1179 VP7 core segment 7 56 NJ Tree

S8 116 NS2 non-structural segment 8 44 NJ Tree

S9 1100 VP6 core segment 9 7 NJ Tree

S10 756 NS3/3A non-structural segment 10 205 NJ Tree

Dr S. J. Lycett
Institute of Biodiversity, Animal Health and Comparative Medicine
University of Glasgow
Room 319, Jarrett Building, 464 Bearsden Road
Glasgow, G61 1QH

Segment	Length	Protein	Location	FASTA	Num.Seqs.	NJ Tree
L1	3500	VP1	core	segment 1	7	NJ Tree
L2	3229	VP2	outer shell	segment 2	55	See individual serotype files
L3	2792	VP3	core	segment 3	22	NJ Tree
M4	1978	VP4	core	segment 4	21	NJ Tree
M5	1751	NS1	non-structural	segment 5	63	NJ Tree
M6	1566	VP5	outer shell	segment 6	32	NJ Tree
S7	1179	VP7	core	segment 7	56	NJ Tree
S8	116	NS2	non-structural	segment 8	44	NJ Tree
S9	1100	VP6	core	segment 9	7	NJ Tree
S10	756	NS3/3A	non-structural	segment 10	205	NJ Tree