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[ Home ] [ Up ] [ BTV-2-seg-2-primers ] [ BTV-S2-Primers-Eurotypes ] [ BTV-S2-Field&vaccine ]
PCR primers designed to detect and identify
Serotypes of BTV found in Europe since
1998
|
BTV-1 |
BTV-4 |
BTV-7 |
BTV-10 |
BTV-13 |
BTV-16 |
BTV-19 |
BTV-22 |
|
BTV-2 |
BTV-5 |
BTV-8 |
BTV-11 |
BTV-14 |
BTV-17 |
BTV-20 |
BTV-23 |
|
BTV-3 |
BTV-6 |
BTV-9 |
BTV-12 |
BTV-15 |
BTV-18 |
BTV-21 |
BTV-24 |
Table 1:
Primers for type-specific amplification of Seg-2 from
BTV-1
by RT-PCR (updated 21st June 2007)
|
BTV-1 primer pair |
Individual forward and
reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify eastern or western strains of
BTV-1 |
|
1A1 |
BTV-1/2/406F
BTV-1/2/968R |
GAGAACARGAARAATATAT |
1220 |
1686 |
[ 1 ] |
|
TYATACGTTGAGAAGTTTTGT |
2906 |
|
1A2 |
BTV-1/2/524F
BTV-1/2/968R |
TAAGTGGATAATMGCWCCGAT |
1572 |
1334 |
[ 1 ] |
|
TYATACGTTGAGAAGTTTTGT |
2906 |
|
1A3 |
BTV-1/2/335F
BTV-1/2/591R |
GRAATCARCGYAGAGATG |
1007 |
765 |
[ 1 ] |
|
TGYTGYCGYGARAGCGCCTG |
1772 |
|
1A4 |
BTV-1/2/529F
BTV-1/2/976R |
GCWCCRATGTTYAAYGCTAA |
1587 |
1343 |
[ 1 ] |
|
GGTCAAGCRGRTYATACRTTGAGAAGT |
2930 |
|
Primers to detect and
identify eastern strains of
BTV-1 |
|
1E 1 |
BTV-1/2/85F
BTV-1/2/815R |
TACGAGGTTATGATGGGAAG |
256 |
2189 |
[ 1 ] |
|
GCACCTCATCTAGCTTGCTAG |
2445 |
|
1E2 |
BTV-1/2/543F
BTV-1/2/778R |
GCACAACGACGGAATGACG |
1629 |
707 |
[ 1 ] |
|
GATGACCTTAAGTTCGTGCG |
2336 |
|
Primers to detect and
identify western strains of
BTV-1 |
|
1W1 |
BTV-1/2/28F
BTV-1/2/830R |
TCACAATAGATGTTGGAACT |
84 |
2408 |
[ 1 ] |
|
GAATTGACTCCCCCATCATATACCGT |
2492 |
|
1W2 |
BTV-1/2/131F
BTV-1/2/733R |
GCAGGAATGTAGCTCACTCG |
394 |
1805 |
[ 1 ] |
|
TTGTACTACGGTAGCGCCACTT |
2199 |
|
Primers to detect and identify the South
African vaccine strain of BTV-1
|
|
1V |
BTV-1/2/28F
BTV-1/2/733R |
TCACAATAGATGTTGGAACT |
84 |
2115 |
[ 1 ] |
|
TTGTACTACGGTAGCGCCACTT |
2199 |
Individual primers are identified by the BTV
serotype (e.g. BTV-1) followed by the number 2 (to indicate segment 2)
then a number to indicate the relative amino acid position of the primer
within VP2, followed by ‘F’ or ‘R’ to indicate forward or reverse
orientation. Primers designed for the other serotypes (tables 2-6) use
a similar nomenclature. Primers were widely evaluated:
See
Mertens et al 2007
Table
2: Primers for
type-specific amplification of Seg-2 from
BTV-2
by RT-PCR (updated
21st June 2007)
|
BTV-1 primer pair |
Individual forward and reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify any eastern or western strains of
BTV-2 |
|
2A |
BTV-2/2/284F
BTV-2/2/842R |
GAKYTRTGTCGGATATTRTCACG |
852 |
1804
|
[ 1 ] |
|
TCGTCGCACACTTCRATAG |
2656 |
|
2A |
BTV-2/2/284F
BTV-2/2/842R |
GAKYTRTGTCGGATATTRTCACG |
852 |
1804
|
[ 1 ] |
|
TCGTCGCACACTTCRATAG |
2656 |
|
2A |
BTV-2/2/284F
BTV-2/2/842R |
GAKYTRTGTCGGATATTRTCACG |
852 |
1804
|
[ 1 ] |
|
TCGTCGCACACTTCRATAG |
2656 |
|
Primers to detect and
identify eastern strains of
BTV-2 |
|
2E |
BTV-2/2/460R |
GCCTAAGTCGCATCGAAAA |
1001 |
381 |
[ 1 ] |
|
GTCCTCATCGCTGTCTGGG |
1382 |
|
Primers to detect and
identify western strains of BTV-2 |
|
2W1
|
BTV-2/2/198F
BTV-2/2/416R |
TATCAGTTAATAGTGCATT |
595 |
653 |
[ 1 ] |
|
TACTAAAKATATACTTCTCCGT |
1248 |
|
2W2
|
BTV-2/2/558F
BTV-2/2/845R |
CTYAAACCGATGACTRATGA |
1674 |
861 |
[ 1 ] |
|
GGTKGAAACAACRTTMAAATT |
2535 |
|
Primers to detect and
identify western strains of BTV-2
but excluding the vaccine or reference strains from South Africa |
|
2W3
|
BTV-2/2/444F
BTV-2/2/633R |
CTAGAGAAAGGCAATCCTTGTGACC |
1334 |
565 |
[ 1 ] |
|
CAGGATGTATCGTCCAGTC |
1898 |
|
Primers to detect and identify vaccine or reference strains from
South Africa of BTV-2
but
will also amplify some other western strains
of BTV-2 |
|
2W4
|
BTV-2/2/30F
BTV-2/2/632R |
TAATACTGGTGTAAAATAT |
92 |
1806 |
[ 1 ] |
|
TCCAGAATGTATCGCCCGGTT |
1898 |
Table 4: Primers for
type-specific amplification of Seg-2 from
BTV-4
by RT-PCR (updated
21st June 2007)
|
BTV-1 primer pair |
Individual forward and reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify western strains of
BTV-4 |
|
4W1 |
BTV-4/2/67F
BTV-4/2/775R |
GCTTAACTATAAACCAACGAGG |
200 |
2125 |
[ 1 ] |
|
GTATCAACCTGACCGCGTCG |
2325 |
|
4W2 |
BTV-4/2/67F
BTV-4/2/841R |
GCTTAACTATAAACCAACGAGG |
200 |
2324 |
[ 1 ] |
|
AACTTGGACGTC
ACAACAGG |
2524 |
|
4W3 |
BTV-4/2/106F
BTV-4/2/919R |
GACGGATGCTAARTGGATGAA |
318 |
2441 |
[ 1 ] |
|
AATACACCTGTAACTGGCCCTC |
2759 |
|
Primers to detect and identify western
strains of BTV-4
(but excluding the Turkish or South
African vaccines) |
|
4F |
BTV-4/2/234F
BTV-4/2/645R |
CTATCATATAACAGRTTCATC |
701 |
1233 |
[ 1 ] |
|
CGTTTGATGTTCTAAGCCTTC |
1934 |
|
Primers to detect and identify the South
African or Turkish vaccine strain of
BTV-4
(but excluding other western strains |
|
4V |
BTV-4/2/233F
BTV-4/2/650R |
CTTATCATACAATAGATWTATT |
701 |
1249 |
[ 1 ] |
|
CATTTGGTGTTCTAAACCCTCA |
1950 |
Table 8: Primers for
type-specific amplification of Seg-2 from
BTV-8
by RT-PCR (updated
21st June 2007)
|
BTV-1 primer pair |
Individual forward and reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify western strains of
BTV-8 |
|
8W1 |
BTV-8/2/710F
BTV-8/2/897R |
GTAGGACGAGCCAGGATTGACGCG |
2130 |
|
[ 1 ] |
|
GATAGAATRCGTTCCCGCCT |
2692 |
|
8W2 |
BTV-8/2/101F
BTV-8/2/500R |
GAATGATGGTCATAGCGAG |
302 |
|
[ 1 ] |
|
CCGATGTGCGCRTYCYTCTC |
1534 |
|
8W3 |
BTV-8/2/276F
BTV-8/2/870R |
TTCGATCAAAGGGAAATCAAGGT |
828 |
|
[ 1 ] |
|
TGTAATTGGCAVGTACCAAAG |
2612 |
|
8W4 |
BTV-8/2/33F
BTV-8/2/623R |
TAGTCGTGTTGAAGAGGAAGGTG |
101 |
|
[ 1 ] |
|
GTTGCTTAGAGAGAGCGCGG |
1770 |
Table 9: Primers for
type-specific amplification of Seg-2 from
BTV-9 by RT-PCR (updated
21st June 2007)
|
BTV-1 primer pair |
Individual forward and reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify any eastern or western strains of
BTV-9 |
|
9A1 |
BTV-9/2/177F
BTV-9/2/852R |
TCTRATAAATAATGGGTTATAT |
533 |
2023 |
[ 1 ] |
|
CCACATARTGAYGAATGATAGAT |
2556 |
|
9A2 |
BTV-9/2/377F
BTV-9/2/485R |
ACGTTGATYGCWRCRGAATG |
1132 |
345 |
[ 1 ] |
|
TSCCWTSDTCRTGAAAGAGT |
1477 |
|
Primers to detect and
identify eastern strains of
BTV-9 |
|
9E1 |
BTV-9/2/245F
BTV-9/2/638R |
ATAGATATGAGCGATCCGG |
687 |
1241 |
[ 1 ] |
|
CTGGTCCACATGGTAGRTC |
1928 |
|
9E2 |
BTV-9/2/113F
BTV-9/2/890R |
GCTATCTGACGCTATGGATG |
340 |
2330 |
[ 1 ] |
|
GCCTTGCTGATCCTATGTTG |
2670 |
|
Primers to detect and
identify western strains of
BTV-9
including the South African reference and
vaccine strains |
|
9W1 |
BTV-9/2/132F
BTV-9/2/713R |
GCGCGGTCAAGTGTGACTTG |
397 |
1743 |
[ 1 ] |
|
GGAATGTGTCAAGTCTATCAG |
2140 |
|
9W2 |
BTV-9/2/205F
BTV-9/2/730R |
ACGCGAGAATGTTGAGGAG |
617 |
1573 |
[ 1 ] |
|
GATATGCGCGACGTCCGTG |
2190 |
Table 16: Primers for
type-specific amplification of Seg-2 from
BTV-16
by RT-PCR (updated
21st June 2007)
|
BTV-1 primer pair |
Individual forward and reverse primers
|
Primer Sequence (5’ to 3’) |
Position on genome segment 2 (NT)
|
Predicted Product Size (bp) |
References |
|
Primers to detect and
identify eastern or western strains of
BTV-16 |
|
16A |
BTV-16/2/273F
BTV-16/2/p792R |
GGAGGRAACTTCGARCGAA |
819 |
1557 |
[ 1 ] |
|
TCACCAAYCCRAAWCGATT |
2376 |
|
Primers to detect and
identify eastern strains of
BTV-16 |
|
16E1 |
BTV-16/2/137F
BTV-16/2/282R |
GGGATGTTTTCAAACACGT |
412 |
434 |
[ 1 ] |
|
GATGTGTGTTCGCTCGAAG |
846 |
|
16E2 |
BTV-16/2/170F
BTV-16/2/341R |
GTCACGTTCACACGGCAA |
509 |
515 |
[ 1 ] |
|
TCGTACGGTGTGTTTTGTGT |
1024 |
|
16E3 |
BTV-16/2/266F
BTV-16/2/924R |
GCGATAAGAGATAMTTGGAT |
798 |
1974 |
[ 1 ] |
|
GCCGAAGGTGCGATCTGGCCG |
2772 |
|
16E4 |
BTV-16/2/151F
BTV-16/2/745R |
CCACGTCATATCATACGAT |
453 |
2181 |
[ 1 ] |
|
GCGAGTCCGACACCTCAAG |
2634 |
|
Primers to detect and
identify western strains of
BTV-16 |
|
16W1 |
BTV-16/2/165F
BTV-16/2/883R |
GTGAGTGTCGTCATGTACG |
500 |
1498 |
[ 1 ] |
|
CGCGGACGCATCCAGCTTC |
1998 |
|
16W2 |
BTV-16/2/308F
BTV-16/2/832R |
GATGGTTAATATGGAAGAG |
891 |
1575 |
[ 1 ] |
|
GATAGCGCCTGCGCACGCAAG |
2466 |
References
Previous primer sets
BTV-2 (all below listed primer sets have been validated with
most related serotype i.e BTV-1)
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BTV-2/2/595-PF |
BTV-2/2/198-PF |
TATCAGTTAATAGTGCATT |
1248-595=653(2A) |
2A set works well with all available BTV-2 isolates
except Indian isolate |
|
BTV-2/2/1248-PR |
BTV-2/2/416-PR |
TACTAAAT/GATATACTTCTCCGT |
|
|
|
BT-2/2/852P-F |
BT-1/2/284P-F |
GAG/TT/CTG/ATGTCGGATATTA/GTCACG |
2656-852=1804(2i) |
2i set works well with all available BTV-2 isolates
including Indian isolate |
|
BT-2/2/2656P-R |
BT-1/2/842P-R |
TCGTCGCACACTTCG/AATAG |
|
|
BTV-4 (all below listed primer sets have been validated with
most related serotypes i.e BTV-10, 11, 13, 17, 20 and 24)
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BTV-4/2/200-PF |
BTV-4/2/67PF |
GCTTAACTATAAACCAACGAGG |
2325-200=2125(4A) |
4A set works well with all available BTV-4 isolates |
|
BTV-4/2/2325-PR |
BTV-4/2/775-PR |
GTATCAACCTGACCGCGTCG |
|
|
|
BTV-4/2/ 2524R |
BTV-4/2/ 2KR |
AACTTGGACGTC ACAACAGG |
2524-200=2324(4B) |
4B set works well with all available BTV-4 isolates.
Better than 4A |
BTV-9 (all below listed primer sets have been validated with
most related serotype i.e BTV-5)
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BTV-9/2/533-PF |
BTV-9/2/177-PF |
TCTG/AATAAATAATGGGTTATAT |
2556-533=2023 (9B) |
9B set worked very well |
|
BTV-9/2/2556-PR |
BTV-9/2/852-PR |
CCACATAA/GTGAT/CGAATGATAGAT |
|
|
|
BTV-9/2/1473-PF |
BTV-9/2/491-PF |
GGC/GAATATATTTCTA/GATGG |
2601-1473=1128(9C) |
9C pair works very well |
|
BTV-9/2/2601-PR |
BTV-9/2/867-PR |
GGAAAACTGATTGGCAAT |
|
|
BTV-16 (all below listed primer sets have been validated with
most related serotype i.e BTV-3 and 13)
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BTV-16/2/798-PF |
BTV-16/2/266-PF |
GCGATAAGAGATAA/CTTGGAT |
2772-798=1974 (16B) |
16B set (without Nigerian isolate) is woking well |
|
BTV-16/2/1273-PF |
BTV-16/2/423-PF |
GGAGAGCCA/T/CGCAACGAAGG |
2772-1273=1499(16D) |
16D set (without Nigerian isolate) works well |
|
BTV-16/2/1417-PF |
BTV-16/2/472-PF |
GAGATGATTCAAAT/CGATAAT |
2772-1417=1355(16F) |
16F set (without Nigerian isolate) works well |
|
BTV-16/2/1806-PF |
BTV-16/2/602-PF |
GGATCCATTATATCCAGG |
2772(924R)-1806=966(16H) |
16H set (without Nigerian isolate) works well |
|
BTV-16/2/2010-PF |
BTV-16/2/670-PF |
GAACGTTGTATGATGTCTCG |
2772(924R)-2010=762(16i) |
16i set (without Nigerian isolate) works well |
|
BTV-16/2/2772-PR |
BTV-16/2/924-PR |
GCCGAAGGTGCGATCTGGCCG |
|
|
|
BTV-16/2/453-PF |
BTV-16/2/151-PF |
CCACGTCATATCATACGAT |
2235-453=1782(16G) |
16G set (without Nigerian isolate) works well |
|
BTV-16/2/2235-PR |
BTV-16/2/745-PR |
GCGAGTCCGACACCTCAAG |
|
|
|
BTV-16/2/819-PF |
BTV-16/2/273-PF |
GGAGGG/AAACTTCGAG/ACGAA |
2376-819=1557(16N) |
16N set (with Nigerian isolate) works well |
|
BTV-16/2/2376-PR |
BTV-16/2/792-PR |
TCACCAAT/CCCA/GAAA/TCGATT |
|
|
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