. 2013 Apr;51(4):1110–1117. doi: 10.1128/JCM.02704-12

Table 2.

Primers and probes

Assay type and primer or exo probe^a	Sequence (5′–3′)^b
DNA assays
BA1 RPA FP	`TACAGGGGATTTATCTATTCCTAGTTCTGAG`
BA1 RPA RP	`GTAGCAAATGTATATTCATCACTCTTCTTAAC`
BA1 RPA P	`GAAAATATTCCATCGGAAAACCAATATTTTCA-BTF-GCTATTTGGTCAGGAT-P`
BA2 RPA FP	`CTGGAACAATAACTCCAATACCACGGAATTCA`
BA2 RPA RP	`GGTGTTTCAAGATTCATGATTTTATATGGCCG`
BA2 RPA P	`TGGCATAACAGGATAACAATAATCAAATAAAAGT-BTF-AAACAAATACCTGTAATTAGC-P`
YP RPA FP	`CCAGTATCGCATTAATGATTTTGAGTTAAATGC`
YP RPA RP	`TCCAGCGTTAATTACGGTACCATAATAACGTGAG`
YP RPA P	`CGACTGGGTTCGGGCACATGATAATGATGAGCACTA-BTF-GAGAGATCTTACTT-P`
VARV RPA FP	`GAGAATCCACAACMGACAAGACKTCSGGAC`
VARV RPA RP	`TTGGCGGTTGATTTAGTAGTGACAATTTCA`
VARV RPA P	`TGTATGAGACAGTGTCTGTGACTGTATGA-BTF-TCTTTATTAGTAATTGGTCC-P`
VACV RPA FP	`ACATACACTAGTGATAGCATTAATACAGTAAG`
VACV RPA RP	`AGATGATGTACTTACTGTAGTGTATGAGACAGT`
VACV RPA P	`TCTTCTTATCAGTAATTGGTTCCGGAGTCTCG-BTF-TGTGGATTCTCCA-P`
RNA assays
EBO RPA FP	`GACGACAATCCTGGCCATCAAGATGATGATCC`
EBO RPA RP	`CGTCCTCGTCTAGATCGAATAGGACCAAGTC`
EBO RPA P	`GATGATGGAAGCTACGGCGAATACCAGAG-BTF-CGGAAAACGGCATG-P`
SUD RPA FP	`CAACTATYCCAGGTGGTGTTGTTGACCCGT`
SUD RPA RP	`GGCTGTCRTCATCGTCGTCGTCCAAATTGAAGA`
SUD RPA P	`CTCCTGTGGTGCCTTCAGCCGAATCCTCG-BTF-CAGGATAATTATTACT-P`
MAR1 RPA FP	`CATGAACATCAGGAAATTCAAGCTATTGCMGARG`
MAR1 RPA RP	`CTAATTTTTCTCGTTTCTGGCTGAGGACGGC`
MAR1 RPA P	`TGTGTGTGATTTCAGTTTTYTGAAGGTGGAAY-BTF-TCTAATATCTTCC-P`
MAR2 RPA FP	`CGACATGAACACCAGGAAATTCAGGCCATCGCC`
MAR2 RPA RP	`CGAGCTAGTTTCTCTCGTTTCTGGCTGAGGAC`
MAR2 RPA P	`AATCTCAGTCTTCTGGAGATGGAACTGTTCTAA-BTF-TTTTCTCTCTTCGTC-P`
SIGV RPA FP	`TGACCATCCTAACTCTGTGACATTCCAAGT`
SIGV RPA RP	`GTTGACAGTGAGCTCTTGAATCTCTGGGTT`
SIGV RPA P	`ACTGATTTCCCTCCGTGTCCTCCCGGTACCAC-BTF-CCAAACTGCCGTTGTG-P`
MARV FPG P	`(dR-FAM)GCCGT-B-CTCAGCCAGAAACGAGARAAAYTAGC(C3-Spacer)`
ZEBO FPG P	`(dR-FAM)GGCG-B-ATACCAGAGTTACTCGGAAAACGGCATGAA-P`
SIG FPG P	`(dR-FAM)TGTC-B-TCCCGGTACCACTATCCAAACTGCCGTTGT-P`

FP or RP, forward or reverse primer; P, probe.

BTF, thymidine nucleotide carrying Blackhole Quencher 1, tetrahydrofuran spacer, and thymidine nucleotide carrying fluorescein; P, 3′phosphate to block elongation.