COMPOSITIONS FOR USE IN IDENTIFICATION OF HERPESVIRUSES

• US 20110200985A1
• Filed: 09/29/2009
• Published: 08/18/2011
• Est. Priority Date: 10/02/2008
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Sampath, Rangarajan, Li, Feng, Hall, Thomas A., Kreft, Rachael, Blyn, Lawrence B., Ecker, David J.
• Application Number:
  US13/122,346
• Publication Number:
  US 20110200985A1
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/705 for herpetoviridae, e.g. herpes simplex, varicella zoster
• CPC Class Codes: C12Q 2563/167 Mass label

Abstract

The present invention relates generally to identification of herpesviruses and provides methods, compositions and kits useful for this purpose when combined, for example, with molecular mass or base composition analysis.

Claims

1. A composition, comprising at least two oligonucleotide primer pairs that are selected from the group consisting of:

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₂₀G₂₃C₂₄T₂₂] base composition from a Herpes simplex 1 virus nucleic acid, a [A₁₉G₂₃C₁₆T₂₁] base composition from a Human herpesvirus 2 nucleic acid, and a [A₁₈G₁₂C₂₅T₂₄] base composition from a Bovine herpesvirus 2 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₆G₁₉C₁₇T₂₁] base composition from a Herpes simplex 1 virus nucleic acid, a [A₁₆G₁₈C₁₉T₂₀] base composition from a Human herpesvirus 2 nucleic acid, and a [A₁₅G₁₇C₁₈T₂₃] base composition from a Bovine herpesvirus 2 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₂₄G₄₃C₃₆T₂₄] base composition from a Herpes simplex 1 virus nucleic acid, a [A₂₆G₃₄C₄₁T₂₆] base composition from a Human herpesvirus 2 nucleic acid, and a [A₂₆G₃₄C₄₁T₂₆] base composition from a Bovine herpesvirus 2 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₉G₃₁C₂₅T₁₇] base composition from a Herpesvirus aotus nucleic acid and a [A₁₆G₉C₂₅T₂₁] base composition from a Human herpesvirus 5 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₆G₂₃C₁₄T₂₂] base composition from a Herpesvirus aotus nucleic acid, a Human herpesvirus 1 nucleic acid, a Human herpesvirus 4 nucleic acid, and a Human herpesvirus 6 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₅G₃₄C₁₉T₃₃] base composition from a Human herpesvirus 1 nucleic acid and a Human herpesvirus 6 nucleic acid;

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₂G₂₂C₁₄T₁₃] base composition from a Bovine herpesvirus 2 nucleic acid and a Human herpesvirus 1 nucleic acid, a [A₁₂G₂₃C₁₄T₁₂] base composition from a Human herpesvirus 2 nucleic acid, and a [A₁₃G₂₀C₁₈T₁₀] base composition from a Human herpesvirus 4 nucleic acid; and

at least one primer pair comprising sequences that are configured to generate amplicons comprising a [A₁₇G₁₇C₂₄T₁₃] base composition from a Herpes simplex 1 virus nucleic acid, a Human herpesvirus 4 nucleic acid, and a Human herpesvirus 5 nucleic acid.

26. A method for identifying a herpesvirus in a sample said method comprising:

(a) obtaining an amplification product by amplifying nucleic acid of a herpesvirus in said sample using the primer pair of claim 1;

(b) measuring the molecular mass of one or both strands of said amplification product;

(c) comparing said molecular mass to a plurality of database-stored molecular masses of strands of amplification products of known herpesviruses; and

d) identifying a match between said molecular mass and at least one of said database-stored molecular masses of amplification products, thereby identifying said herpesvirus.

27. The method of claim 26 wherein each member of said primer pair has at least 70% sequence identity with a corresponding member of a primer pair selected from the group consisting of:

SEQ ID NOs;

26;

40, 46;

6, 8;

50, 20;

34, 24;

30, 27;

7, 48;

28, 54;

43, 19;

51, 35;

3, 45;

53, 38;

12, 56;

13, 18;

52, 41;

21, 49;

17, 16;

25, 22;

42, 31;

15, 5;

55, 37;

47, 36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44, 29;

9 and 39;

14.

28. The method of claim 26 wherein said nucleic acid comprises a gene selected from the group consisting of nuclear antigen type 1, nuclear antigen type 2, nuclear antigen type 3, latent membrane protein, and DNA polymerase.

29. The method of claim 26 wherein said molecular mass is determined by mass spectrometry.

30. A method for identifying a herpesvirus in a sample, said method comprising:

(a) obtaining an amplification product by amplifying nucleic acid of a herpesvirus in said sample using the purified primer pair of claim 1;

(b) measuring the molecular mass of one or both strands of said amplification product;

(c) determining the base composition of said amplification product from said molecular mass;

(d) comparing said base composition to a plurality of database-stored base compositions of strands of amplification products of known herpesviruses; and

(e) identifying a match between said base composition and at least one of said database-stored molecular masses of amplification products, thereby identifying said herpesvirus.

31. The method of claim 30 wherein each member of said primer pair has at least 70% sequence identity with a corresponding member of a primer pair selected from the group consisting of:

SEQ ID NOs;

26;

40, 46;

6, 8;

50, 20;

34, 24;

30, 27;

7, 48;

28, 54;

43, 19;

51, 35;

3, 45;

53, 38;

12, 56;

13, 18;

52, 41;

21, 49;

17, 16;

25, 22;

42, 31;

15, 5;

55, 37;

47, 36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44, 29;

9 and 39;

14.

32. The method of claim 30 wherein said nucleic acid comprises a gene selected from the group consisting of nuclear antigen type 1, nuclear antigen type 2, nuclear antigen type 3, latent membrane protein, and DNA polymerase.

33. The method of claim 30 wherein said molecular mass is determined by mass spectrometry.

2. A purified oligonucleotide primer pair for identifying a herpesvirus in a sample, said primer pair comprising a forward primer and a reverse primer, each configured to hybridize to nucleic acid of two or more different herpesvirus species or strains in a nucleic acid amplification reaction which produces an amplification product between about 29 to about 200 nucleobases in length, said amplification product comprising portions corresponding to a forward primer hybridization region, a reverse primer hybridization region and an intervening region having a base composition which varies among amplification products produced from nucleic acid of said two or more different herpesvirus species or strains, said base composition of said intervening region providing a means for identifying said herpesvirus.

3. The primer pair of claim 2, wherein said herpesvirus is selected from the group consisting of:

Alcelaphine herpesvirus 1, Ateline herpesvirus 3, Atlantic bottlenose dolphin gammaherpesvirus, Baboon cytomegalovirus, Baboon gamma-herpesvirus, Bacteriophage BFK20, Bacteriophage Mx8, Bovine herpesvirus 1, Bovine herpesvirus 1, Bovine herpesvirus 2, Bovine herpesvirus 4, Bovine herpesvirus 5, Bovine herpesvirus type 1.1, Bovine lymphotropic herpesvirus, Callithrix penicillata lymphocryptovirus 1, Callitrichine herpesvirus 3, Caprine herpesvirus 2, Cebus albifrons lymphocryptovirus 1, Cercopithecine herpesvirus 1, Cercopithecine herpesvirus 15, Cercopithecine herpesvirus 16, Cercopithecine herpesvirus 2, Cercopithecine herpesvirus 3, Cercopithecine herpesvirus 5, Cercopithecine herpesvirus 8, Cercopithecus cephus cytomegaloVirus 1, Chlorocebus rhadinovirus 1, Chlorocebus rhadinovirus 2, Colobus guereza cytomegalovirus 1, Colobus guereza lymphocryptovirus 1, Columbid herpesvirus 1, Crocidura russula cytomegalovirus 1, Cytomegalovirus, Epstein-Barr virus, Equid herpesvirus 1, Equid herpesvirus 2, Equid herpesvirus 4, Equus zebra rhadinovirus 1, Fibropapilloma-associated turtle herpesvirus, Florida green turtle herpesvirus, Gorilla gorilla lymphocryptovirus 1, Gorilla lymphocryptovirus 1, Gorilla rhadinovirus 1, Green turtle herpesvirus, Hawaiian green turtle herpesvirus, Herpesvirus papio 2, Hexaprotodon liberiensis lymphotropic herpesvirus 1, Human herpesvirus 1, Human herpesvirus 2, Human herpesvirus 3, Human herpesvirus 3 (strain Dumas), Human herpesvirus 4, Human herpesvirus 5, Human herpesvirus 6, Human herpesvirus 6B, Human herpesvirus 7, Human herpesvirus 8, Hylobates lar lymphocryptovirus 1, Hylobates leucogenys lymphocryptovirus 1, Hylobates nomascus leucogenys lymphocryptovirus 1, Hylobates pileatus lymphocryptovirus, Loggerhead turtle herpesvirus, Macaca fascicularis cytomegalovirus 1, Macaca fascicularis lymphocryptovirus 1, Macaca fuscata lymphocryptovirus 1, Macaca fuscata rhadinovirus, Macaca mulatta rhadinovirus 17577, Macaca nemestrina rhadinovirus 2, Mandrillus cytomegalovirus, Mandrillus herpesvirus 1, Murid herpesvirus 4, Mycobacterium phage Bxz1, Olive ridley turtle herpesvirus, Ovine herpesvirus 2, Pan troglodytes herpesvirus 6, Pan troglodytes rhadinovirus 1, Pan troglodytes rhadinovirus 1a, Pongo pygmaeus cytomegalovirus 1, Porcine cytomegalovirus, Porcine cytomegalovirus B6, Porcine lymphotropic herpesvirus 1, Porcine lymphotropic herpesvirus 2, Porcine lymphotropic herpesvirus 3, Psittacid herpesvirus 1, Rat cytomegalovirus Maastricht, Rhesus cytomegalovirus strain 68-1, Rhesus monkey rhadinovirus H26-95, Saimiriine herpesvirus 2, Suid herpesvirus 1, Sus barbatus lymphotropic herpesvirus 1, Tupaiid herpesvirus 1, unidentified herpesvirus, Vervet cytomegalovirus CSG, and Vulture herpesvirus.

4. The primer pair of claim 2 wherein each member of said primer pair has at least 70% sequence identity with a corresponding member of a primer pair selected from the group consisting of:

SEQ ID NOs;

26;

40, 46;

6, 8;

50, 20;

34, 24;

30, 27;

7, 48;

28, 54;

43, 19;

51, 35;

3, 45;

53, 38;

12, 56;

13, 18;

52, 41;

21, 49;

17, 16;

25, 22;

42, 31;

15, 5;

55, 37;

47, 36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44, 29;

9 and 39;

14.

5. The primer pair of claim 4 wherein said forward primer and said reverse primer are about 14 to about 40 nucleobases in length.

6. The primer pair of claim 4, wherein said forward primer or said reverse primer or both further comprise a non-templated thymidine residue on the 5′

-end.

7. The primer pair of claim 4, wherein said forward primer or said reverse primer or both further comprise at least one molecular mass modifying tag.

8. The primer pair of claim 4, wherein said forward primer or said reverse primer or both further comprise at least one modified nucleobase.

9. The primer pair of claim 8, wherein said modified nucleobase is 5-propynyluracil or 5-propynylcytosine.

10. The primer pair of claim 8, wherein said modified nucleobase is a mass-modified nucleobase.

11. The primer pair of claim 10, wherein said mass-modified nucleobase is 5-iodo-cytosine.

12. The primer pair of claim 8, wherein said modified nucleobase is a universal nucleobase.

13. The primer pair of claim 12, wherein said universal nucleobase is inosine.

37. A system, comprising:

(a) a mass spectrometer configured to detect one or more molecular masses of an amplification product of claim 13;

(b) a database of known molecular masses and/or known base compositions of amplification products of herpesviruses; and

(c) a controller operably connected to said mass spectrometer and to said database said controller configured to match said molecular masses of said amplification product with a measured or calculated molecular mass of a corresponding amplification product of herpesviruses.

38. The system of claim 37 wherein said database of known molecular masses and/or known base compositions of amplification products of herpesviruses includes amplification products defined by one or more primer pairs wherein each member of said one or more primer pairs has at least 70% sequence identity with a corresponding member of a corresponding primer pair selected from the group consisting of:

SEQ ID NOs;

26;

40, 46;

6, 8;

50, 20;

34, 24;

30, 27;

7, 48;

28, 54;

43, 19;

51, 35;

3, 45;

53, 38;

12, 56;

13, 18;

52, 41;

21, 49;

17, 16;

25, 22;

42, 31;

15, 5;

55, 37;

47, 36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44, 29;

9 and 39;

14.

14. An isolated amplification product for identification of a herpesvirus, said amplification product produced by a process comprising:

a) amplifying nucleic acid of a herpesvirus in a reaction mixture comprising a primer pair, said primer pair comprising a forward primer and a reverse primer, each configured to hybridize to nucleic acid of two or more different herpesviruses in a nucleic acid amplification reaction, said amplification product having a length of about 29 to about 200 nucleobases and comprising portions corresponding to a forward primer hybridization region, a reverse primer hybridization region and an intervening region having a base composition which varies among amplification products produced from nucleic acid of said two or more different herpesviruses, said base composition of said intervening region providing a means for identifying said herpesvirus; and

b) isolating said amplification product from said reaction mixture.

15. The amplification product of claim 14 wherein said isolating step is performed using an anion exchange resin linked to a magnetic bead.

16. The amplification product of claim 14 wherein each member of said primer pair has at least 70% sequence identity with a corresponding member of a primer pair selected from the group consisting of:

SEQ ID NOs;

26;

40, 46;

6, 8;

50, 20;

34, 24;

30, 27;

7, 48;

28, 54;

43, 19;

51, 35;

3, 45;

53, 38;

12, 56;

13, 18;

52, 41;

21, 49;

17, 16;

25, 22;

42, 31;

15, 5;

55, 37;

47, 36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44, 29;

9 and 39;

14.

17. The amplification product of claim 16 wherein said forward primer and said reverse primer are about 14 to about 40 nucleobases in length.

18. The amplification product of claim 16, wherein said forward primer or said reverse primer or both further comprise a non-templated thymidine residue on the 5′

-end.

19. The amplification product of claim 16, wherein said forward primer or said reverse primer or both further comprise at least one molecular mass modifying tag.

20. The amplification product of claim 16, wherein said forward primer or said reverse primer or both further comprise at least one modified nucleobase.

21. The amplification product of claim 20, wherein said modified nucleobase is 5-propynyluracil or 5-propynylcytosine.

22. The amplification product of claim 20, wherein said modified nucleobase is a mass-modified nucleobase.

23. The amplification product of claim 22, wherein said mass-modified nucleobase is 5-iodo-cytosine.

24. The amplification product of claim 22, wherein said modified nucleobase is a universal nucleobase.

25. The amplification product of claim 24, wherein said universal nucleobase is inosine.

34. A kit comprising one or more purified primer pairs for identifying a herpesvirus in a sample, each member of said one or more primer pairs having at least 70% sequence identity with a corresponding member of one or more primer pairs selected from the group consisting of:

SEQ ID NOs;

36;

11, 59;

60, 32;

57, 33;

1, 10;

23, 58;

4, 2;

44 and 29;

9.

35. The kit of claim 34 further comprising deoxynucleotide triphosphates.

36. The kit of claim 34 wherein one or more of said deoxynucleotide triphosphates is 13C-enriched.