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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.
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Virology Journal

ISSN: 1743-422X