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Table 1 PCR primers

From: Development of a real-time QPCR assay for the detection of RV2 lineage-specific rhadinoviruses in macaques and baboons

Primer1

Gene Target

Sequence2

RV2 QPCR Assay (Figure 2)

  

RV2a

RV2 ORF 60

5'-TCTGAATATGTCACATCCGTTCATA-3'

RV2b

RV2 ORF 59/60 intergenic

5'-GGCCCGGAAAATGAGTAACA-3'

RV2-FAM3

RV2 ORF 60 and 59/60 intergenic

5'-(6-FAM)-TGATCTGTAGTCCCCATGTGTCC-(BHQ-1)-3'

OSM QPCR Assay (Figure 3)

  

OSMa

Exon 3 OSM

5'-CCTCGGGCTCAGGAACAAC-3'

OSMb

Exon 3 OSM

5'-GGCCTTCGTGGGCTCAG-3'

OSM-FAM

Exon 3 OSM

5'-(6-FAM)-TACTGCATGGCCCAGCTGCTGGACAA-(BHQ-1)-3'

ORF 59/60 CODEHOP Primers

  

RDELa4

ORF 60 bias5 KSHV

5'-CTTGCCAACGATTACATTTCCAGRGAYGARCT-3'

SRDEa4

ORF 60 bias RRV

5' CTGGCTAACGACTACATCTCCAGRGAYGARCT-3'

NFFEa

ORF 60 bias KSHV

5'-GGCAGTTTCAAGGCTGTGAATTTYTTYGARCG-3'

PQFVb6

ORF 59 bias KSHV

5'-CCGTAAGAAATGGTGGTCCTGACRAAYTGNGG-3'

QFVRb6

ORF 59 bias RRV

5'-CCGTAGGCGATGGTCGTCCTAACRAAYTGNGG-3'

CFICb

ORF 59 bias RRV

5'-TACAAAATACAGCGAGTGATANATRAARCA-3'

Gene-Specific Primer

  

MPVDb

ORF 59 (RFHV/KSHV)7

5'-TGAAAATCCACAGGCATGAT-3'

  1. 1The terminal "a" or "b" in the primer name indicates the plus or minus sense of the gene transcription, respectively.
  2. 2IUB code for ambiguous nucleotides: R = A or G; Y = C or T; N = A, C, G, or T
  3. 3FAM indicates a TaqMan dual-labeled probe with the fluorescent dye 6-FAM at the 5' end and the "black hole quencher" (BHQ) dye at the 3' end.
  4. 4These CODEHOP primers target the same motif but are biased differently (see below).
  5. 5"bias" indicates that the 5' consensus region of the CODEHOP primer was derived from a particular sequence" see [20].
  6. 6These CODEHOP primers target the same motif but are biased differently.
  7. 7This primer sequence is identical to the RFHVMn, RFHVMm and KSHV sequences
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Virology Journal

ISSN: 1743-422X