Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1

Wang, Hongmei; Hou, Peili; Zhao, Guimin; Yu, Li; Gao, Yu-wei; He, Hongbin

doi:10.1186/s12917-018-1644-4

Table 1 The sequences of primers and probes designed for screening in the study

From: Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1

Primer/probe set Name		Sequence(5′ → 3′)	The location on accession number	Product sizes (bp)
	F2	ATGGAGCACCTGAGGCAGCACTGGACAACA	3452–3481	221
A1	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	203
	R1	[Biotin]CGTTGAGAAGGGCACAGTCGTATTGAAACA	3643–3672
	F2	ATGGAGCACCTGAGGCAGCACTGGACAACA	3452–3481	258
A2	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	250
	R2	[Biotin]GCACGAGGAGTTCTTGGATCTCCGTGGCTC	3680–3709
	F2	ATGGAGCACCTGAGGCAGCACTGGACAACA	3452–3481	352
A3	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	229
	R3	[Biotin]GCAGGGGCAATAATTTTCTGCTTGTGTCTG	3774–3803
	F1	CACCTGAGGCAGCACTGGACAACACGAGCAA	3458–3488	215
A4	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	203
	R1	[Biotin]GCCGTAGTTGAAGGAGGCAGGAAGCTGTGC	3643–3672
	F1	CACCTGAGGCAGCACTGGACAACACGAGCAA	3458–3488	252
A5	P1	[FAM] CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	240
A5	R2	[Biotin]GCACGAGGAGTTCTTGGATCTCCGTGGCTC	3680–3709
A6 (Optimal set)	F1	CACCTGAGGCAGCACTGGACAACACGAGCAA	3458–3488	346
	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	334
	R3	[Biotin]GCAGGGGCAATAATTTTCTGCTTGTGTCTG	3774–3803
	F3	TGAGGCAGCACTGGACAACACGAGCAACCC	3462–3461	211
A7	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	203
	R1	[Biotin]GCCGTAGTTGAAGGAGGCAGGAAGCTGTGC	3643–3672
	F3	TGAGGCAGCACTGGACAACACGAGCAACCC	3462–3461	248
A8	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	240
	R2	[Biotin]GCACGAGGAGTTCTTGGATCTCCGTGGCTC	3680–3709
	F3	TGAGGCAGCACTGGACAACACGAGCAACCC	3462–3461	342
A9	P1	[FAM]CACTGGACAACACGAGCAACCCCACTGCTTA[dSpacer] TATAAAGCACCGTTCACA[C3-spacer]	3470–3519	334
	R3	[Biotin]GCAGGGGCAATAATTTTCTGCTTGTGTCTG	3774–3803
	F1	AAAAGCAACCCATTACCCGCCTGGCACTCC	3582–3611	285
As1	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	271
As1	R2	[Biotin]GACTCTTCCCCGTAGGTTGTCTTCCCGTTG	3837–3866
As2	F1	AAAAGCAACCCATTACCCGCCTGGCACTCC	3582–3611	145
	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	131
	R3	[Biotin]GGGAGTGCCAGGCGGGTAATGGGTTGCTTT	3697–3726
	F2	AACCCAACCGCCTACCAAAAGCAACCCATT	3566–3595	153
As3	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	123
	R1	[Biotin]CGGTGTAAGGGAGTGCCAGGCGGGTAATGG	3689–3718
	F2	AACCCAACCGCCTACCAAAAGCAACCCATT	3566–3595	301
As4	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	271
	R2	[Biotin]GACTCTTCCCCGTAGGTTGTCTTCCCGTTG	3837–3866
	F2	AACCCAACCGCCTACCAAAAGCAACCCATT	3566–3595	161
As5	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	131
	R1	[Biotin]CGGTGTAAGGGAGTGCCAGGCGGGTAATGG	3689–3718
	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	445
As6	P2	[FAM]TGAAACTCACACAGCTCAAGAACACCCAAACT[dSpacer] TTGATCTTATGCAAATC[C3-spacer]	3378–3427	341
	R1	[Biotin]CGGTGTAAGGGAGTGCCAGGCGGGTAATGG	3689–3718
	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	593
As7	P2	[FAM]TGAAACTCACACAGCTCAAGAACACCCAAACT[dSpacer] TTGATCTTATGCAAATC[C3-spacer]	3378–3427	489
	R2	[Biotin]GACTCTTCCCCGTAGGTTGTCTTCCCGTTG	3837–3866
	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	453
As8	P2	[FAM]TGAAACTCACACAGCTCAAGAACACCCAAACT[dSpacer] TTGATCTTATGCAAATC[C3-spacer]	3378–3427	349
As8	R3	[Biotin]GGGAGTGCCAGGCGGGTAATGGGTTGCTTT	3697–3726
As9 (Optimal set)	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	286
	P2	[FAM]TGAAACTCACACAGCTCAAGAACACCCAAACT[dSpacer] TTGATCTTATGCAAATC[C3-spacer]	3378–3427	182
	R4	[Biotin]GAGAAGTAGTACGTCGCAGACCGAAGTAGCG	3530–3559
	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	445
As10	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3378–3427	341
	R1	[Biotin]CGGTGTAAGGGAGTGCCAGGCGGGTAATGG	3689–3718
	F3	CGAATCAGCAGACCCAGTTACCACCACAGT	3274–3303	593
As11	P1	[FAM]ACCCGCCTGGCACTCCCTTACACCGCTCCC[dSpacer]ACCGTGTGCTTGCAACAGT[C3-spacer]	3596–3645	271
	R2	[Biotin]GACTCTTCCCCGTAGGTTGTCTTCCCGTTG	3837–3866
	F1	CAACACCACCAACCCAACGGCGTACCATAA	3570–3599	161
O1	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	141
	R1	[Biotin]GAGCCAGCACTTGGAGATCGCCTCTCACGT	3701–3730
	F1	CAACACCACCAACCCAACGGCGTACCATAA	3570–3599	343
O2	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	323
	R2	[Biotin]CAAGGACTGCTTTACAGGTGCCACTATTTT	3883–3912
	F1	CAACACCACCAACCCAACGGCGTACCATAA	3570–3599	210
O3	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	190
	R3	[Biotin]TTGATGGCACCGTAGTTGAAAGAAGTAGGC	3751–3779
	F2	GGAGCACCTGAAGCAGCCTTGGACAACACC	3549–3578	182
O4	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	141
	R1	[Biotin]GAGCCAGCACTTGGAGATCGCCTCTCACGT	3701–3730
	F2	GGAGCACCTGAAGCAGCCTTGGACAACACC	3549–3578	364
O5	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	323
O5	R2	[Biotin]CAAGGACTGCTTTACAGGTGCCACTATTTT	3883–3912
O6 (Optimal set)	F2	GGAGCACCTGAAGCAGCCTTGGACAACACC	3549–3578	231
	P1	[FAM]CGTACCATAAGGCGCCGCTTACCCGGCTTA[dSpacer] ATTGCCCTACACGGCACCA[C3-spacer]	3590–3639	190
	R3	[Biotin]TTGATGGCACCGTAGTTGAAAGAAGTAGGC	3751–3779
	F3	GGGGACCTTACCTGGGTGCCAAATGGAGCA	3524–3553	217
O7	P2	[FAM]CAAATGGAGCACCTGAAGCAGCCTTGGACAA[dSpacer]ACCACCAACCCAACGGCGTAC[C3-spacer]	3542–3596	189
	R1	[Biotin]GAGCCAGCACTTGGAGATCGCCTCTCACGT	3701–3730
	F3	GGGGACCTTACCTGGGTGCCAAATGGAGCA	3524–3553	389
O8	P2	[FAM]CAAATGGAGCACCTGAAGCAGCCTTGGACAA[dSpacer]ACCACCAACCCAACGGCGTAC[C3-spacer]	3542–3596	371
	R2	[Biotin]CAAGGACTGCTTTACAGGTGCCACTATTTT	3883–3912
	F3	GGGGACCTTACCTGGGTGCCAAATGGAGCA	3524–3553	256
O9	P2	[FAM]CAAATGGAGCACCTGAAGCAGCCTTGGACAA[dSpacer]ACCACCAACCCAACGGCGTAC[C3-spacer]	3542–3596	238
O9	R3	[Biotin]TTGATGGCACCGTAGTTGAAAGAAGTAGGC	3751–3779

Note: F:forward primer, R reverse primer, P probe, FAM Carboxyfluorescein, dSpacer A tetrahydrofuran residue, C3-spacer 3’-block

Back to article page

ISSN: 1746-6148

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Veterinary Research

Contact us