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Table 4 CODEHOP and gene-specific primers developed for cloning the complete DNA polymerase gene of novel macaque rhadinoviruses.

From: CODEHOP-mediated PCR – A powerful technique for the identification and characterization of viral genomes

Primer Gene Target Bias Sense 5'>3' Sequence (degenerate codons are in lower case)1
   3' Core 5' Clamp   
CODEHOP 2      
FREYA (32) gB4 γHV3 KSHV4 + TTTGACCTGGAGACTATGttymgngartayaa
GGMA (128) gB γHV KSHV + ACCTTCATCAAAAATCCCttnggnggnatgyt
CVNVA (64) DNA pol γHV KSHV + GACGACCGCAGCGTGTGCGTGaaygtnttyggnca
CVNVB (64) DNA pol γHV KSHV - TAAAAGTACAGCTCCTGCCCGaanacrttnacrca
YFDKB (16) DNA pol γHV KSHV - TTAGCTACTCCGTGGAGCagyttrtcraarta
GDWE2B (8) ORF 10 γHV KSHV - GAAGTGGCAGTTGGAGAGGCTGACCTCCcartcncc
  1. 1 See legend to Table 1 for the I.U.B. code.
  2. 2 See Figure 11 for the relative positions of the conserved sequence blocks from which the CODEHOPs were derived. The degree of degeneracy, ie the number of individual primers in the pool, is given in parentheses.
  3. 3 The CODEHOPs were derived from the alignment of conserved genes within the gammaherpesvirus subfamily.
  4. 4 The 5' Clamp region was derived from the KSHV sequence flanking the 3' core in order to target genes from RFHV, the macaque homolog of KSHV.