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Table 1 CODEHOPs developed for herpesvirus screens targeting the DNA polymerase

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

CODEHOPS (degeneracy)1

Bias2

Sense

5'>3' Sequence(degenerate codons are in lower case)3

 

3' Core

5' Clamp

  

"TVG-IYG" Assay 4

    

DFA (512)

All HV (IHV, HHV6,7)

NA5

+

Gayttygcnagyytntaycc

ILK (1024)

All HV

 

+

TCCTGGACAAGCAGcarnysgcnmtnaa

TGV (256)

All HV (IHV, HHV6,7)

-6

+

TGTAACTCGGTGtayggnttyacnggngt

IYG (48)

All HV (IHV, AlHV1, RRV)

-

-

CACAGAGTCCGTrtcnccrtadat

KG1 (128)

All HV

-

-

GTCTTGCTCACCAGntcnacnccytt

"DFASA-GDTD1B" Assay 7

    

DFASA (256)

All HV (IHV, HHV6,7)

-

+

GTGTTCGACttygcnagyytntaycc

VYGA (256)

All HV (IHV)

-

+

ACGTGCAACGCGGTGtayggnktnacngg

GDTD1B (64)

All HV

-

-

CGGCATGCGACAAACACGGAGTCngtrtcnccrta

"QAHNA" Assay 7

    

QAHNA (48)

αHV γHV (IHV, βHV)

(CMV)

+

CCAAGTATCathcargcncayaa

"SLYP" Assay 8

    

SLYP1A (64)

All HV (CMV, EHV2)

-

+

TTTGACTTTGCCAGCCTGtayccnagyatnat

SLYP2A (128)

CMV (All other HV)

-

+

TTTGACTTTGCCAGCCTGtayccntcnatnat

CODEHOP Predicted 9

    

HNLCA (32)

All HV (IHV)

CODEHOP10

+

TCCATCATCCAGGCCcayaayytntg

VYG1A (128)

All HV (IHV)

CODEHOP

+

GCAACGCGGTGTACggnktnacngg

YGDTB (16)

All HV

CODEHOP11

-

CGGCATGCCATGAACATGGAGTCCGTrtcnccrta

KGVDB (32)

All HV

CODEHOP

-

CTTCCGCACCAGGTCnacnccytt

  1. 1 The degree of degeneracy, ie the number of individual primers in the pool, is given in parentheses.
  2. 2 Bias indicates the reliance on a specified subset of sequences for determination of the 3' degenerate core or 5' consensus clamp. Sequences which are biased against by the choice of nucleotide sequences are indicated in parentheses (see the multiple sequence alignments from which the primers were derived in Figures 3-6).
  3. 3 IUB code: Y = T, C; R = A, G; K = G, T; M = A, C; H = A, C, T not G; N = A, C, G, T.
  4. 4 [8]
  5. 5 NA, not applicable
  6. 6 (-), no specific design bias
  7. 7 [9]
  8. 8 Primers predicted manually.
  9. 9 Primers predicted using the CODEHOP software.
  10. 10 Clamp sequence was predicted by the CODEHOP software using default codon usage table and thus had no inherent bias design
  11. 11Underlined sequences have been added to the primer predicted by the CODEHOP software (see legend to Figure 4) Abbreviations: HV, herpesvirus; αHV, alphaherpesvirus; βHV, betaherpesvirus; γHV, gammaherpesvirus; AhlHV1, alcelaphine herpesvirus 1; CMV, cytomegalovirus; EHV2, equine herpesvirus-2, HHV6, human herpesvirus 6; HHV7, human herpesvirus 7; IHV, ictalurid herpesvirus (catfish)
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Virology Journal

ISSN: 1743-422X