COMPOSITIONS FOR USE IN IDENTIFICATION OF TICK-BORNE PATHOGENS

• US 20110143358A1
• Filed: 05/29/2009
• Published: 06/16/2011
• Est. Priority Date: 05/30/2008
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Eshoo, Mark W., Matthews, Heather E., Crowder, Christopher D., Sampath, Rangarajan, Blyn, Lawrence B., Ecker, David J.
• Application Number:
  US12/995,429
• Publication Number:
  US 20110143358A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention relates generally to the field of genetic identification and quantification of tick borne pathogens and provides methods, compositions and kits useful for this purpose when combined with molecular mass or base composition analysis.

Claims

1. A composition, comprising at least one purified oligonucleotide primer pair that comprises forward and reverse primers, wherein said primer pair comprises nucleic acid sequences that are substantially complementary to nucleic acid sequences of two or more different tick-borne pathogens and/or or endosymbionts, wherein said primer pair is configured to produce amplicons comprising different base compositions that correspond to said two or more different bioagents.

2. The composition of claim 1, wherein said primer pair is configured to hybridize with conserved regions of said two or more different bioagents and flank variable regions of said two or more different bioagents.

3. The composition of claim 1, wherein said forward and reverse primers are about 15 to 35 nucleobases in length, and wherein the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with a sequence selected from the group consisting of SEQ ID NOS:

1-18 and the reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;

19-36.

4. The composition of claim 1, wherein said primer pair is selected from the group of primer pair sequences consisting of:

SEQ ID NOS;

1;

19, 2;

20, 3;

21, 4;

22, 5;

23, 6;

24, 7;

25, 8;

26, 9;

27, 10;

28;

11;

29, 12;

30, 13;

31, 14;

32, 15;

33, 16;

34, 17;

35 and 18;

36.

5. The composition of claim 1, wherein said forward and reverse primers are about 15 to 35 nucleobases in length, and wherein:

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

1, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

19;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

2, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

20;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

3, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

21;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

4, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

22;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

5, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

23;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

6, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

24;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

7, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

25;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

8, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

26;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

9, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

27;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

10, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

28;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

11, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

29;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

12, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

30;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

13, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

31;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

14, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

32;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

15, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

33;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

16, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

34;

the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

17, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

35; and

/or the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

18, and the reverse primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with the sequence of SEQ ID NO;

36.

6. The composition of claim 1, wherein said different base compositions identify said two or more different bioagents at genus, species, or sub-species levels.

7. The composition of claim 1, wherein said two or more amplicons are 45 to 200 nucleobases in length.

8. A kit comprising the composition of claim 1.

9. The composition of claim 1, wherein said different bioagents are selected from the group consisting of:

a Spirochete, an alphaproteobacteria, a Francisella sp., Coxiella burnetii, a Flavivirus, Borrelia miyamotoi, Borrelia burgdorferi type 1, Borrelia burgdorferi type 2, Borrelia lonestari, Spotted Fever Group Rickettsia variant 1, Spotted Fever Group Rickettsia variant 2, Spotted Fever Group Rickettsia variant 3, Rickettsia amblyommii, Anaplasma phagocytophilum, Spiroplasma ixodetis, Ehrlichia variant 1, Wolbachia variant 1, Bartonella variant 1, Bartonella variant 2, Bartonella variant 3, Francisella genus, or combinations thereof.

10. The composition of claim 1, wherein said primer pair is configured to hybridize with one or more nucleic acid sequences selected from the group consisting of:

flagellin, rplB, gyrB, hbb, rnpA, gltA, rpoB, asd, gale, icd, IS1111A, S. kunkeii TraE-like gene, 16S rRNA gene, 23S rRNA gene and RdRp nucleic acids.

11. The composition of claim 1, wherein a non-templated T residue on the 5′

-end of said forward and/or reverse primer is removed.

12. The composition of claim 1, wherein said forward and/or reverse primer further comprises a non-templated T residue on the 5′

-end.

13. The composition of claim 1, wherein said forward and/or reverse primer comprises at least one molecular mass modifying tag.

14. The composition of claim 1, wherein said forward and/or reverse primer comprises at least one modified nucleobase.

15. The composition of claim 14, wherein said modified nucleobase is 5-propynyluracil or 5-propynylcytosine.

16. The composition of claim 14, wherein said modified nucleobase is a mass modified nucleobase.

17. The composition of claim 16, wherein said mass modified nucleobase is 5-Iodo-C.

18. The composition of claim 14, wherein said modified nucleobase is a universal nucleobase.

19. The composition of claim 18, wherein said universal nucleobase is inosine.

20. A kit, comprising at least one purified oligonucleotide primer pair that comprises forward and reverse primers that are about 20 to 35 nucleobases in length, and wherein said forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with a sequence selected from the group consisting of SEQ ID NOS:

1-18, and said reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;

19-36.

21. A method of determining a presence of a tick-borne pathogen and/or or endosymbiont in at least one sample, the method comprising:

(a) amplifying one or more segments of at least one nucleic acid from said sample using at least one purified oligonucleotide primer pair that comprises forward and reverse primers that are about 20 to 35 nucleobases in length, and wherein said forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with a sequence selected from the group consisting of SEQ ID NOs;

1-18, and said reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOs;

19-36 to produce at least one amplification product; and

(b) detecting said amplification product, thereby determining said presence of said tick-borne pathogen and/or or endosymbiont in said sample.

22. The method of claim 21, wherein (b) comprises detecting a molecular mass of said amplification product.

23. The method of claim 21, wherein (b) comprises determining a base composition of said amplification product, wherein said base composition identifies the number of A residues, C residues, T residues, G residues, U residues, analogs thereof and/or mass tag residues thereof in said amplification product, whereby said base composition indicates the presence of tick-borne pathogen and/or or endosymbiont in said sample or identifies said tick-borne pathogen and/or or endosymbiont in said sample.

24. The method of claim 23, comprising comparing said base composition of said amplification product to calculated or measured base compositions of amplification products of one or more known tick-borne pathogens and/or or endosymbionts present in a database with the proviso that sequencing of said amplification product is not used to indicate the presence of or to identify said tick-borne pathogen and/or or endosymbiont, wherein a match between said determined base composition and said calculated or measured base composition in said database indicates the presence of or identifies said tick-borne pathogen and/or or endosymbiont.

26. A system, comprising:

(a) a mass spectrometer configured to detect one or more molecular masses of amplicons produced using at least one purified oligonucleotide primer pair that comprises forward and reverse primers, wherein said primer pair comprises nucleic acid sequences that are substantially complementary to nucleic acid sequences of two or more different tick-borne pathogen and/or or endosymbiont bioagents; and

(b) a controller operably connected to said mass spectrometer, said controller configured to correlate said molecular masses of said amplicons with one or more tick-borne pathogen and/or or endosymbiont bioagent identities.

27. The system of claim 26, wherein said tick-borne pathogen and/or or endosymbiont bioagent identities are at genus, species, and/or sub-species levels.

28. The system of claim 27, wherein said forward and reverse primers are about 15 to 35 nucleobases in length, and wherein the forward primer comprises at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identity with a sequence selected from the group consisting of SEQ ID NOS:

1-18, and the reverse primer comprises at least 70% sequence identity with a sequence selected from the group consisting of SEQ ID NOS;

19-36.

29. The system of claim 27, wherein said controller is configured to determine base compositions of said amplicons from said molecular masses of said amplicons, which base compositions correspond to said one or more tick-borne pathogen and/or or endosymbiont bioagent identities.

30. The system of claim 27, wherein said controller comprises or is operably connected to a database of known molecular masses and/or known base compositions of amplicons of known tick-borne pathogen and/or or endosymbiont bioagents produced with the primer pair.