Biological specimen collection/transport compositions and methods
Disclosed are compositions for collecting, storing, and transporting populations of nucleic acids from biological specimens, and clinical, forensic, or environmental samples. Also disclosed are methods for using these compositions as one-step formulations for killing pathogens, inactivating nucleases, and releasing polynucleotides from other cellular components within the sample, and stabilizing the nucleic acids prior to further processing or assay. In particular embodiments, the invention provides a single, one-step, sample collection/transport/storage formulation containing a known quantity of a non-genomic, nucleic acid carrier molecule that serves as an internal reference control to monitor the fidelity of the collection/transportation medium, and measure the integrity of nucleic acids subsequently isolated and purified from the processed sample.
1. A one-step method of maintaining the integrity of a biological sample for nucleic acid testing in solution, comprising providing an aqueous mixture at a pH of about 6 to 7 that contains:
a control nucleic acid sequence,
one or more chaotropes;
one or more detergents;
one or more reducing agents;
one or more chelators; and
one or more buffers,
collectively and in an amount sufficient to denature proteins, inactivate nucleases, kill pathogens, and release nucleic acid from an organism or cell contained within the biological sample when contacted with the biological sample in solution, wherein:
upon contact with the biological sample in solution, the released nucleic acid and the control nucleic sequence acid are each detectable in solution by nucleic acid testing for at least 7 days when stored at a temperature of greater than 4° C. and the control nucleic acid sequence is distinguishable from the released nucleic acid; and
the control nucleic acid sequence and the released nucleic acid in solution are detectable by a single nucleic acid testing.
2. The method of claim 1 , wherein the control nucleic acid sequence does not hybridize to released nucleic acid under stringent hybridization conditions.
3. The method of claim 2 , wherein the control nucleic acid sequence does not ordinarily occur within a mammalian genome, or a genome of a bacterium, fungus, protozoan, or virus that is pathogenic to a mammal.
4. The method of claim 3 , wherein the control nucleic acid sequence is synthetic and from about 40 to about 900 nucleotides in length.
5. The method of claim 4 , wherein the control nucleic acid is present in the mixture at a concentration of about 1 pg to 1 μg/ml of mixture.
6. The method of claim 5 , wherein the control nucleic acid is a calibration control for the nucleic acid testing.
7. The method of claim 1 , wherein the nucleic acid testing is PCR analysis.
8. The method of claim 7 , wherein the control nucleic acid sequence and the released nucleic acid are detectable by a single PCR analysis.
9. The method of claim 1 , wherein the pH of the mixture is from about 6.2 to 6.9.
10. The method of claim 1 , wherein the released nucleic acid and the control nucleic sequence acid are each detectable by nucleic acid testing for at least 14 days.
11. The method of claim 10 , wherein the released nucleic acid and the control nucleic acid sequence are each detectable by nucleic acid testing for at least 21 days.
12. The method of claim 1 , wherein the released nucleic acid and the control nucleic sequence acid are each detectable by nucleic acid testing for at least 7days when the temperature is about 10° C. or greater.
13. The method of claim 12 , wherein the released nucleic acid and the control nucleic sequence acid are each detectable by nucleic acid testing for at least 7days when the temperature is about 14° C. or greater.
14. The method of claim 12 , wherein the released nucleic acid and the control nucleic sequence acid are each detectable by nucleic acid testing for at least 21 days when the temperature is about 10° C. or greater.
15. The method of claim 1 , wherein the one or more chaotropes are present in an amount from about 0.5 M to about 6 M; the one or more detergents are present in an amount from about 0.1% to about 1% (wt./vol.); the one or more reducing agents are present in an amount from about 0.5 mM to about 0.3 M; the one or more chelators are present in an amount from about 0.01 mM to about 1 mM; and the one or more buffers are present in an amount from about 1 mM to about 1 M.
16. The method of claim 15 , wherein:
the one or more chaotropes comprise guanidine thiocyanate, guanidine isocyanate, guanidine hydrochloride, or any combination thereof;
the one or more detergents comprise sodium dodecyl sulfate, lithium dodecyl sulfate, sodium taurodeoxycholate, sodium taurocholate, sodium glycocholate, sodium deoxycholate, sodium cholate, sodium alkylbenzene sulfonate, N-lauroyl sarcosine, or any combination thereof;
the one or more reducing agents comprise 2-mercaptoethanol, tris(2-carboxyethyl) phosphine, dithiothreitol, dimethylsulfoxide, or any combination thereof; the one or more chelators comprise ethylene glycol tetra acetic acid, hydroxyethylethylenediaminetriacetic acid, diethylene triamine penta acetic acid, N,N-bis(carboxymethyl)glycine, ethylenediaminetetraacetic, citrate anhydrous, sodium citrate, calcium citrate, ammonium citrate, ammonium bicitrate, citric acid, diammonium citrate, ferric ammonium citrate, lithium citrate, or any combination thereof; and
the one or more buffers comprise tris(hydroxymethyl) aminomethane, citrate, 2-(N-morpholino)ethanesulfonic acid, N,N-Bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, 1,3-bis(tris(hydroxymethyl)methyl amino)propane, 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid, 3-(N-morpholino) propanesulfonic acid, bicarbonate, phosphate, or any combination thereof.
17. The method of claim 1 , wherein the mixture further comprises:
one or more surfactants or defoaming agents at about 0.0001% to about 0.3% (wt./vol.); and;
one or more short-chain alkanols at about 1% to 25% (vol./vol.).
18. The method of claim 17 , wherein the one or more surfactants or defoaming agents is selected from the group consisting of a silicone polymer, a polysorbate, and any combination thereof; and the one or more short-chain alkanols is selected from the group consisting of methanol, ethanol, propanol, butanol, pentanol, hexanol, and any combination thereof.
19. The method of claim 18 , wherein the mixture comprises:
about 4 M guanidine thiocyanate; about 30 mM sodium citrate; about 0.25% (wt./vol.) sodium dodecyl sulfate; about 0.25% (wt./vol.) N-lauroyl sarcosine, sodium salt; about 0.1 M 2-mercaptoethanol; and about 0.1% silicone polymer (wt./vol.); or
about 3 M guanidine thiocyanate; about 1 mM TCEP; about 10 mM sodium citrate; about 0.5% N-lauroyl sarcosine; about 0.0002% silicone polymer; about 100 mM 2-amino-2-hydroxymethyl-propane-1,3-diol (TRIS); and about 0.1 mM EDTA; or
about 1 M to about 4 M guanidine thiocyanate; about 0.5 mM to 10 mM TCEP; about 1 mM to 100 mM sodium citrate; about 0.1% to about 1% SDS or NLS; about 0.001% to about 0.0001% of a silicone polymer, about 10 mM to about 500 mM TRIS, about 0.1 mM to about 1 mM APCA, EDTA, EGTA, HEDTA, DTPA, NTA, or citrate; and about 10% to about 25% ethanol (vol./vol.); or
about 3 M guanidine thiocyanate; 1 mM TCEP; about 10 mM sodium citrate; about 0.5% N-lauroyl sarcosine, sodium salt; about 0.0002% of a silicone polymer; about 100 mM TRIS; about 0.1 mM EDTA; and about 10% to about 25% ethanol (vol./vol.).
20. The method of claim 1 , wherein 5% or less of the released nucleic acid is degraded after the at least 7 days.
21. The method of claim 1 , further comprising contacting the biological sample with the mixture.
22. The method of claim 21 , further comprising performing nucleic acid testing of the released nucleic acid and the control nucleic acid sequence.
23. The method of claim 22 , wherein the control nucleic acid sequence comprises:
a first sequence domain that specifically binds to a labeled probe of about 12 to about 35 nucleotides in length that is specific for detection of the control nucleic acid sequence;
a second sequence domain that specifically binds to a forward PCR amplification primer of about 15 to about 35 nucleotides in length; and
a third sequence domain that specifically binds to a reverse PCR amplification primer of about 15 to about 35 nucleotides in length, wherein the second and third sequence domains are operably positioned to facilitate a PCR-directed amplification of at least a first portion of the control nucleic acid sequence from the forward and reverse primers under conditions effective to amplify the at least a first portion.
24. A one-step method of maintaining the integrity of a biological sample in solution for nucleic acid testing, comprising:
providing an aqueous mixture at a pH of about 6 to 7 that contains:
a control nucleic acid sequence,
one or more chaotropes;
one or more detergents;
one or more reducing agents;
one or more chelators; and
one or more buffers,
contacting the biological sample in solution to an amount of the mixture that is sufficient to denature proteins, inactivate nucleases, kill pathogens, and release nucleic acid from an organism or cell contained within the biological sample,
wherein the released nucleic acid and the control nucleic sequence acid are each detectable in solution by nucleic acid testing for at least 7 days when stored at a temperature of greater than 10° C. and the control nucleic acid sequence is distinguishable from the released nucleic acid, and
wherein the control nucleic acid sequence and the released nucleic acid are detectable by a single nucleic acid testing.
25. The method of claim 24 , wherein the mixture further comprises:
one or more surfactants or defoaming agents at about 0.0001% to about 0.3% (wt./vol.); and;
one or more short-chain alkanols at about 1% to 25% (vol./vol.).
26. The method of claim 24 , wherein the released nucleic acid comprises a sequence identifiable as derived from influenza virus.
27. The method of claim 24 , wherein the released nucleic acid comprises a sequence identifiable as derived from tuberculosis bacteria.
28. The method of claim 24 , wherein the contacting is performed in one vessel and, after contact, the biological sample is non-infectious for transport.
29. The method of claim 24 , wherein, after the contacting, the biological sample does not require refrigeration before the nucleic acid testing.
30. The method of claim 24 , further comprising:
performing the nucleic acid testing on the released nucleic acid and determining the presence or absence of a pathogen in the biological sample.
31. The method of claim 30 , wherein the nucleic acid testing is a single PCR analysis.
32. The method of claim 30 , wherein the pathogen is virus or bacteria.
33. The method of claim 32 , wherein the virus or bacteria is influenza virus or tuberculosis bacteria.
34. A one-step method of maintaining the integrity of a biological sample in solution for nucleic acid testing to determine the presence or absence of a pathogen, comprising:
providing an aqueous mixture at a pH of about 6 to 7 that contains:
a control nucleic acid sequence, one or more chaotropes;
one or more detergents;
one or more reducing agents;
one or more chelators; and
one or more buffers,
contacting in one step the biological sample in solution to an amount of the mixture that is sufficient to denature proteins, inactivate nucleases, kill pathogens, and release nucleic acid from an organism or cell contained within the biological sample, wherein the released nucleic acid and the control nucleic sequence acid are each detectable in solution by nucleic acid testing for at least 2 days when stored at a temperature of greater than 10° C. and the control nucleic acid sequence is distinguishable from the released nucleic acid; and
performing nucleic acid testing on the released nucleic acid and the control nucleic acid sequence, wherein the nucleic acid testing is a PCR analysis;
determining the amount of released nucleic acid present in the sample from the amount of control nucleic acid sequence present in the mixture; and
determining the presence or absence of the pathogen in the biological sample.
35. The method of claim 34 , wherein the mixture further comprises:
one or more surfactants or defoaming agents at about 0.0001% to about 0.3% (wt./vol.); and;
one or more short-chain alkanols at about 1% to 25% (vol./vol.).
36. The method of claim 34 , further comprising transporting the contacted biological sample before performing nucleic acid testing wherein the contacted biological sample is non-infectious for transportation.
37. The method of claim 34 , wherein the released nucleic acid is present at 0.1 pg and detectable at a C T value of about 36.
38. The method of claim 34 , wherein the released nucleic acid is present at 1 pg and detectable at a C T value of about 33.
39. The method of claim 34 , wherein the released nucleic acid is detectable at a C T value that is reduced by at least 5% as compared to the C T value obtained in the absence of the mixture.
40. The method of claim 39 , wherein the released nucleic acid is detectable at a C T value that is reduced by at least 10% as compared to the C T value obtained in the absence of the mixture.