A phylogenetic analysis of Bovine Viral Diarrhoea Virus (BVDV) isolates from six different regions of the UK and links to animal movement data

Booth, Richard E; Thomas, Carole J; El-Attar, Laila MR; Gunn, George; Brownlie, Joe

doi:10.1186/1297-9716-44-43

Veterinary Research

Table 2 Strain allocation table

From: A phylogenetic analysis of Bovine Viral Diarrhoea Virus (BVDV) isolates from six different regions of the UK and links to animal movement data

Sample	Closest 5′UTR reference strain	% Identity to 5′UTR reference strain	Closest N^proreference strain	% Identity to N^proreference strain
1-1	1e	95	1a	83
1-2	1e	95	1a	83
1-3	1e	95	-	-
2-1	1a	98	1a	92
2-5	1a	98	1a	92
2-6	1a	98	1a	92
2-7	1a	98	1a	92
2-8	1a	96	1a	90
2-9	1a	98	1a	92
2-10	1a	96	1a	90
2-11	1a	97	1a	92
2-12	1a	96	1a	90
5-1	1a	95	1a	91
15-1*	1a/1j	95 to both	1a	90
18-1	1b	97	1b	95
18-2	1b	97	1b	95
18-3	1b	97	1b	95
18-4	1b	97	1b	95
18-5	1b	97	1b	95
18-6	1b	97	1b	95
19-1	-	-	1a	93
20-1*	1a/1j	96 to both	1a	92
20-2*	1a/1j	96 to both	1a	91
20-3*	1a/1j	96 to both	1a	91
26-1 ⁺	1a	96	1a	91
26-2 ⁺	1a	96	1a	91
26-3 ⁺	1a	96	1a	91
27-1*	1a/1j	95 to both	1a	92
33-1 ^#	1a	94	1a	91
33-3 ^#	1a	95	1a	92
34-1 ^#	1a	95	1a	92
37-1* ^#	1a/1j	95 to both	1a	88
37-2* ^#	1a/1j	95 to both	1a	88
37-3* ^#	1a/1j	95 to both	1a	88
37-4* ^#	1a/1j	95 to both	1a	88
37-5* ^#	1a/1j	95 to both	1a	88
38-1	1a	97	1a	92
40-1	1a	99	1a	92
40-2	1a	96	1a	92
40-3	1a	99	1a	92
40-4	1a	96	1a	92
40-5	1a	96	1a	93
40-6	1a	99	1a	92
40-7	1a	96	1a	93
40-8	1a	96	1a	92
41-1	1a	95	1a	92
41-2	1a	95	1a	92
41-3	1a	95	1a	92
41-4	1a	95	1a	92
42-1^	1j	95	1a	81
42-2^	1j	95	-	-
43-1	-	-	1a	92
43-2 ⁺	1a	96	1a	92
43-3 ⁺	1a	96	1a	92
43-4 ⁺	1a	96	1a	92
43-5 ⁺	1a	96	1a	92
43-6 ⁺	1a	96	1a	92
43-7 ⁺	1a	96	1a	92
43-8 ⁺	1a	96	1a	92
44-1 ^+#	1a	95	1a	93
44-2* ^#	1a/1j	94 to both	1a	93
45-1 ^#	1a	95	1a	92
46-1	1a	96	1a	90
47-1	1a	97	1a	92
48-1	1a	96	1a	91
48-2	1a	96	1a	91
48-3	1a	96	1a	91
48-4	1a	96	1a	91
48-5	1a	96	-	-
48-6	1a	96	1a	91
48-7	1a	96	1a	91
48-8	1a	96	1a	91
48-9	1a	96	1a	91
48-10	1a	96	1a	91
49-3	1a	96	1a	93
50-1	1a	98	1a	92
50-2	1a	98	1a	91
56-1* ^#	1a/1j	94 to both	1a	92
56-2* ^#	1a/1j	94 to both	1a	92
56-3 ^+#	1a	94	1a	92
56-4* ^#	1a/1j	94 to both	1a	92
56-5* ^#	1a/1j	94 to both	1a	92
57-1	1a	97	1a	92
57-2	1a	97	1a	92
58-1	1i	98	1i	98
58-2	1i	98	1i	98
59-1 ⁺	1a	96	1a	92
59-2	1a	98	1a	92
60-1*	1a/1j	94 to both	1a	90
61-1 ⁺	1a	96	1a	92
62-1	-	-	1a	92
62-2* ^#	1a/1j	94 to both	-	-
62-3* ^#	1a/1j	94 to both	1a	91
63-1*	1c/1a/1j	95 to all	1a	93
64-1 ⁺	1a	96	1a	84
65-1 ⁺	1a	95	1a	92
66-1	1a	97	1a	93
67-1	1d	97	1d	90
67-2	1d	97	1d	90
68-1	1e	98	-	-
69-1	1i	97	-	-
70-1	1a	95	1a	92
70-2	1a	95	1a	92
71-1	1b	98	1b	94

The table indicates the percentage identity of the closest reference strain to the field isolate investigated. Reference strains used are described in Table 3. Where discrepancies or high nucleotide identity occurs with multiple reference strains, this is noted as follows: * indicates isolates with equal 5′UTR nucleotide sequence identity to both BVDV 1a and 1j reference strains, ⁺ indicates isolates with 1% less 5′UTR nucleotide identity to BVDV 1j reference strains than to 1a reference strains, ^ indicates isolates with 1% higher 5′UTR identity to BVDV 1j reference strains than to either 1a or 1c reference strains, ^# indicates isolates with 1% less 5′UTR nucleotide identity to BVDV 1c reference strains than to 1a reference strains, – indicates that no sequence was obtained. (GenBank Accession numbers for the 5′UTR and N^pro regions sequenced for this paper are KF023272-KF023470).

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ISSN: 1297-9716

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