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[ Home ] [ Up ] [ BTV-2-seg-2-primers ] [ BTV-S2-Primers-Eurotypes ] [ BTV-S2-Field&vaccine ]
RT-PCR
primers to distinguish vaccine a field strains of European BTV serotypes
(08/07/2003:
data provided by Sushila Maan, Alan Samuel and Peter Mertens ) Available
as Word file
BTV-1
Field Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BTV-1F/2/1629-PF |
BTV-1F/2/543-PF |
GCACAACGACGGAATGACG |
2336-1629=707(1V-A) |
This pair (1V-A) works well and not pick up vaccine
and African strains but picks up European, Asian and Australian isolates |
|
BTV-1F/2/2336-PF |
BTV-1F/2/778-PR |
GATGACCTTAAGTTCGTGCG |
|
|
BTV-1 Vaccine Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-1V/2/84P-F |
BT-1V/2/28P-F |
TCACAATAGATGTTGGAACT |
2199-84=2115(1V-A)
2492-84=2408(1V-B)
|
(1V-A) picks up only vaccine strain
(1V-B) picks up vaccine+African strains |
|
BT-1V/2/394P-F |
BT-1V/2/131P-F |
GCAGGAATGTAGCTCACTCG |
2199-394=1805(1V-C)
2492-394=2098(1V-D)
|
(1V-C) picks up vaccine+African strains
(1V-D) not good, cannot differentiate |
|
BT-1V/2/2199P-R |
BT-1V/2/733P-R |
TTGTACTACGGTAGCGCCACTT |
|
|
|
BT-1V/2/2492P-R |
BT-1V/2/830P-R |
GAATTGACTCCCCCATCATATACCGT |
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BTV-2 Field Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-2F/2/1334P-F |
BT-2F/2/444P-F |
CTAGAGAAAGGCAATCCTTGTGACC |
1898-1334-565(2F-C) |
(2F-C) works well |
|
BT-2F/2/1898P-R |
BT-2F/2/633P-R |
CAGGATGTATCGTCCAGTC |
|
|
BTV-2 Vaccine Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-2V/2/92P-F |
BT-2V/2/30P-F |
TAATACTGGTGTAAAATAT |
1898-92=1806(2V-original) |
(2V-original) works well |
|
BT-2V/2/1898R |
BT-2V/2/632R |
TCCAGAATGTATCGCCCGGTT |
|
|
BTV-4 European Field Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-4F/2/701P-F |
BT-4F/2/234P-F |
CTATCATATAACAGATTCATC |
1934-701=1233(4F-original) |
(4F-original) primer pair worked well |
|
BT-4F/2/1934P-R |
BT-4F/2/645P-R |
CGTTTGATGTTCTAAGCCTTC |
|
|
BTV-4 Vaccine Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-4V/2/701P-F |
BT-4V/2/233P-F |
CTTATCATACAATAGATT/ATATT |
1950-701=1249(4V-C) |
This primer pair (4V-C) works well and these are from same region in
genome as BTV-4 field strain specific primers |
|
BT-4V/2/1950P-R |
BT-4V/2/650P-R |
CATTTGGTGTTCTAAACCCTCA |
|
|
BTV-9 European Field Strains
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-9F/2/340P-F |
BT-9F/2/113P-F |
GCTATCTGACGCTATGGATG |
2670-340=2330(9F-original) |
This pair (9F-original) works well |
|
BT-9F/2/2670P-R |
BT-9F/2/890P-R |
GCCTTGCTGATCCTATGTTG |
|
|
BTV-9 Vaccine Strain specific primers
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-9V/2/397P-F |
BT-9V/2/132P-F |
GCGCGGTCAAGTGTGACTTG |
2140-397=1743bp |
|
|
BT-9V/2/2140P-R |
BT-9V/2/713P-R |
GGAATGTGTCAAGTCTATCAG |
|
|
|
BTV-9V/2/617-PF |
BTV-9V/2/205-PF |
ACGCGAGAATGTTGAGGAG |
2190-617=1573 |
|
|
BTV-9V/2/2190-PR |
BTV-9V/2/730-PR |
GATATGCGCGACGTCCGTG |
|
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BTV-16 Field Strains ( in BTV-16 differentiation of
field and vaccine strains is not possible, some primer pairs have been tried
which are listed below)
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-16F/2/102P-F |
BT-16F/2/34P-F |
GATGGAGCCAGAGGATGGCG |
2465-102=2363(16F-original) |
problem of cross reaction with this pair |
|
BT-16F/2/2465P-R |
BT-16F/2/822P-R |
GAATCGCGCTCGCGCATGCG |
|
|
|
BT-16F/2/222P-F |
BT-16F/2/74P-F |
TGATGGGGAAGTTTTACCGCGCATT |
1981-222=1759(16F-A) |
problem of cross reaction with this pair |
|
BT-16F/2/1981P-R |
BT-16F/2/660P-R |
CGGGAAACTCATACGTAACGTCACTATCA |
|
|
BTV-16 Vaccine Strains
|
Primer designation (nt) |
Primer designation (aa) |
Primer sequence (5’-3’) |
Product size (bp) |
Remarks |
|
BT-16V/2/487P-F |
BT-16V/2/162P-F |
GCGTGGGTGTTGTCACGTTCACA |
2467-487=1980(16V-original) |
problem of cross reaction with this pair |
|
BT-16V/2/2467P-R |
BT-16V/2/822P-R |
GGATCGCGCTCGCACACGCG |
|
|
|
BT-16V/2/498P-F |
BT-16V/2/166P-F |
GCGTGGGTGTTGTCACGTTCAC |
2348-498=1850(16V-B) |
problem of cross reaction with this pair |
|
BT-16V/2/2348P-R |
BT-16V/2/783P-R |
GCCCACCTCAGCGGGTATG |
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