# Patent

## Title
Method of pooling and/or concentrating biological specimens for analysis

## Abstract

The present invention provides methods for concentrating and pooling liquid suspensions of biological specimens containing analytes of interest in a dry state. The dried biological specimens containing analytes of interest are reconstituted and released from the matrix for subsequent analysis in concentrated form.

## Background
CROSS REFERENCES TO RELATED APPLICATIONS
This application claims benefit of priority to U.S. Provisional Application No. 61/174,720, filed May 1, 2009, which is incorporated by reference in its entirety herein.


FIELD OF THE INVENTION
This invention relates generally to methods for pooling and concentrating biological specimens containing analytes of interest in a dry state. The invention further provides methods for recovery of the biological specimens containing analytes of interest for subsequent research analysis and testing in a concentrated state for improved sensitivity of detection.
BACKGROUND OF THE INVENTION
Biological specimens are often collected, transported and stored for analysis of the levels and concentrations of various analytes contained therewithin. Conventionally, liquid suspensions of biological specimens are stored in sealed airtight tubes under refrigeration. Liquid sample collection, handling, transportation and storage has many problems associated with it, for example: the cost of refrigeration (typically by dry ice) in remote collection centers; the risk of container breakage or leakage which causes loss of sample and the danger of infection; sample instability during shipment and storage; refusal of transport carriers to accept liquid biohazard shipments; and collection of adequate sample volume to ensure quantities compatible with laboratory methods of subsequent analyses. The costs of addressing the above problems are substantial.
Dried blood spot (DBS) and dried plasma spot (DPS) sampling on filter paper are alternative methods to the liquid sampling procedures, and have been used worldwide with some success. Since the 1980s, manufacturers such as Schleicher and Schuell Corp., Bio-Rad, Boehringer Mannheim Corp., and Whatman. Inc., have been producing filter papers for DBS and DPS sampling. In using these commercially available biological sampling filter paper systems, a blood or plasma spot is placed in one or more designated areas of the filter paper, allowed to dry, and then mailed along with a test request form to the laboratory. Commonly used filter papers are known to those of ordinary skill in the art, such as Whatman 3 MM, GF/CM30, GF/QA30, S&S 903, GB002, GB003, or GB004. Several categories of blotting materials for blood specimen collection are available, e.g., S&S 903 cellulose (wood or cotton derived) filter paper and Whatman glass fiber filter paper. However, certain disadvantages have been associated with these commercially available filter papers. Specifically, certain of these commercially available and commonly used materials lack characteristics which provide precision values and accuracy that are preferred for carrying out certain biological assays.
Genetic material can be extracted and isolated from DBSs in sufficient quantities for use in genetic analysis. For instance, DBS has been used for the detection of prenatal human immunodeficiency virus (HIV) infection by the polymerase chain reaction (PCR) (Cassol, et al., J. Clin Microbiol. 30 (12): 3039-42, 1992). DPS and DBS have also been used for HIV RNA detection and quantification (Cassol, et al., J. Clin. Microbiol. 35: 2795-2801, 1997; Fiscus, et al., J. Clin. Microbiol. 36: 258-60, 1998: O'Shea, et al., AIDS 13: 630-1, 1999; Biggar, et al., J. Infec. Dis. 180 1838-43, 1999; Brambilla, et al., J. Clin. Microbiol. 41(5): 1888-93, 2003); HIV DNA detection and quantification (Panteleefe, et al., J. Clin. Microbiol. 37: 350-3, 1999; Nyambi, et al., J. Clin. Microbiol. 32: 2858-60, 1994); and HIV antibody detection (Evengard, et al., AIDS 3: 591-5, 1989; Gwinn, et al., JAMA 265: 1704-08, 1991). HCV RNA detection and genotyping are also reported using DBS (Solmone et al., J. Clin. Microbio. 40 (9): 3512-14, 2002). Although these studies provide a good correlation with titers using DPS or DBS is obtained as compared with conventional liquid plasma samples, a loss of viral titers may occur after room temperature storage (Cassol, et al., J. Clin. Microbiol. 35: 2795-2801, 1997; Fiscus, et al., J. Clin. Microbiol. 36: 258-60. 1998). DBS and DPS samples are clearly less expensive and less hazardous to transport than liquid samples.
However, the procedure of analyte microextraction from DBS and DPS on filter paper suffers from a number of disadvantages. For example, the fibers and other components of the filters become dislodged into the reconstitution solution, and require further centrifugation separation and/or can impede the ability to isolate the genetic material, such as by blocking genetic material from adhering to a separation column. Such prior microextraction procedures require a high standard of technical assistance, and even then do not consistently provide results with a desired level of sensitivity and specificity. Moreover, reconstitution of DBS and DPS samples by conventional means results in dilution of the analyte of interest, as compared to its originally collected concentration in a fluid suspension, decreasing the sensitivity of any subsequent analysis.
Furthermore, the sample volume used for DBS and DPS on filter paper is limited, typically to 50 μl spots, and considerable difficulty in analyte detection can be encountered, particularly when the concentration of the desired analyte material is low in the sample. Also in the prior art, there is a lack of deliberate inhibition of enzymes and chemicals which degrade the analytes, such as genetic material contained therewithin. Even in the presence of a bacteriostatic agent there are conditions that permit enzymatic, nonenzymatic and autolytic breakdown of the genetic material. Furthermore, microextraction of genetic material from DBS or DPS on filter papers is considerably more difficult if absorption of high molecular weight DNA or RNA is required. Although the introduction of new material and transportation methods continuously improve the ways samples are handled, the quantity and quality of the sample available for subsequent analysis are still of great concern to researchers and clinicians alike.
Thus, there is a need for a safe, convenient and simple device for collection, storage and transportation of liquid suspension of biological specimens containing analytes of interest in a dry state, especially in large field studies and for application in settings where collection, centrifugation, storage and shipment can be difficult, as is often the case in developing countries. In addition, there is a need for improved recovery of the biological specimens for subsequent analysis that provides precision values and accuracy of detection of the analytes of interest contained therewithin.
Further, there is a need for a method for efficiently testing collected and stored blood resources for pathogens and other conditions which render a particular blood resource unsuitable for use in blood transfusion. As new pathogens and diseases are identified, blood resources (e.g., blood, plasma, blood cells, platelets, and other blood components) need to be re-screened for the presence of the pathogen or disease. Such a process is extremely expensive for organizations which store blood resources, such as blood banks and clinics. In order to avoid analyzing individual donor samples separately, blood banks will often test batches of samples together in a method known as “pooling.” Pooling involves combining individual samples into a common container, allowing the samples to mix, and then testing a volume of the mixed pool for the presence of an analyte of interest. If the substance is detected, individual samples from the pool are tested for the analyte.
One problem with current pooling methods is the loss of sensitivity caused by the dilution of the individual samples. If a sample contains the analyte of interest, the analyte will be diluted by a factor of x, where x equals the number of samples in the pool. For example, if an analyte is present in a sample at a concentration of 1 mg/ml and 10 samples are pooled, the analyte will be present in the pool at a concentration of 0.1 mg/ml. Because the analyte potentially can be diluted to a level lower than the threshold detection level (which would result in a false negative test result), regulatory agencies such as the U.S. Food and Drug Administration place limits on the quantity of samples that may be pooled in a batch. For example, a blood bank may be allowed to combine 8, 16, or 24 individual samples in a pool. Unfortunately, false negatives may be reported even when regulatory dilution limits are followed. The consequences of a false negative test report are substantial since the transfusion of a blood resource containing the pathogen, such as HIV, may infect the recipient. As such, it would be desirable to provide a method of effectively and efficiently screening biological resources such as for the presence of such a pathogen, disease, or condition without compromising the sensitivity of the screening.
SUMMARY OF THE INVENTION
This invention fulfills in part the need to provide a safe, convenient and simple method for concentrating and/or pooling liquid suspensions of biological specimens containing analytes of interest. The invention also fulfills in part the need to recover biological specimens containing analytes of interest for subsequent analysis that provides more desirable sensitivity and/or specificity of detection. More particularly, the present invention provides a novel methodology for concentrating and/or pooling one or more biological specimens utilizing a matrix to dry the biological specimen prior to rehydration. The present invention provides a methodology that allows for biological testing of detection and analysis of rehydrated biological specimens without the need for refrigerated or frozen shipping and storage.
In one aspect, the present invention provides a method of concentrating a plurality of unique fluid samples containing a biological specimen for subsequent analysis. The plurality of unique fluid samples, as used herein, refers to either a plurality of fluid samples obtained from multiple sources which are pooled and may also be concentrated, or a plurality of fluid samples obtained from a single source (e.g., blood from one person), which can be concentrated, as described herein. In one aspect, the method comprises the following steps: (a) applying onto a matrix a representative sample from each of the plurality of unique fluid samples, each representative sample comprising a biological specimen; (b) drying the matrix containing the representative samples; and (c) reconstituting the representative samples with a controlled volume of a reconstitution fluid, wherein the controlled volume of the reconstitution fluid is less than the combined volume of the representative samples. The invention further provides for the additional step of analyzing a testing volume of the reconstituted representative samples for an analyte of interest, wherein the testing volume is less than the volume of the reconstituted representative samples.
In one embodiment, the controlled volume is substantially equal to the volume of a representative sample. In another embodiment, the testing volume is substantially equal to the controlled volume of reconstitution fluid divided by the combined volume of the representative samples. In another embodiment, the analyte of interest is present in the testing volume in a concentration commensurate with one of the plurality of unique fluid samples.
The method may be performed utilizing a device suitable for collecting, storing or transporting a biological specimen containing analytes of interest. More particularly, the device comprises a sealable container defining an interior space having side walls, a bottom and a lid which may be opened. In one preferred embodiment, the invention provides a container having a threaded screw cap. The device further comprises a matrix inside the container. The matrix absorbs at least 0.1 ml of a liquid suspension of biological specimens, and preferably equal to or greater than 1.0 ml. In certain embodiments, the device also has a desiccant inside the container in vaporous communication with the matrix.
In another preferred embodiment, the invention includes a dry solid matrix for storage of a liquid suspension of biological specimens which absorbs at least 5 ml of the liquid suspension. In another embodiment, the matrix is at least 50% porous, and can be compressed by at least 50% of the volume of the matrix to release a portion of the liquid suspension of biological specimen stored in the matrix. In another embodiment, the matrix is at least 75% porous and is compressible by at least 75% of the volume of the matrix. In preferred embodiments, the matrix is porous and three-dimensional in a variety of different shapes. Preferably, the shape of the matrix is a cylinder, cube, sphere, pyramid, cone or other shapes suitable for absorption and fitting inside a container.
The invention also provides that the matrix is made from an absorbent material. The absorbent material includes, but is not limited to, cellulose acetate fibers, wood or cotton derived cellulose, nitrocellulose, carboxymethylcellulose, hydrophilic polymers including polypropylene, polyester, polyamide, carbohydrate polymers, polytetrafluoroethylene, glass fiber, nylon, and combinations thereof.
The invention also provides that the device includes a matrix that is removable from the container. In preferred embodiments, the matrix is removably mounted in a holder on the lid of a container. In one of the preferred embodiments, the matrix is removably mounted in an extension of a screw cap that attaches to the threads of the container tube.
According to the invention, the analytes of interest include, but are not limited to, nucleic acids, proteins, carbohydrates, lipids, whole cells, cellular fragments, whole virus or viral fragments, and antibodies or antibody fragments. In preferred embodiments, the analytes of interest are nucleic acids including either or both DNA and RNA molecules. According to the invention, the biological specimens include, but are not limited to, whole blood, plasma, urine, saliva, sputum, semen, vaginal lavage, bone marrow, cerebrospinal fluid, other physiological or pathological body liquids, or any of the combinations thereof. Preferably, the biological specimen is human or animal body fluid, more preferably, the biological specimen is the whole blood, most preferably, the analytes are nucleic acids, including either or both DNA and RNA molecules. In one of the preferred embodiments, the analytes of interest are nucleic acids and the biological specimens comprise at least 500 ng to 1 μg either or both DNA or RNA molecules. In yet another preferred embodiment, the biological specimen is contained in liquid suspension. According to the present invention, the liquid suspension includes but is not limited to cell suspension, liquid extracts, tissue homogenates, media from DNA or RNA synthesis, saline or any combinations thereof. The analytes of interest can be contained in biological specimens from any source including medical, industrial or environmental samples.
In another aspect the present invention provides a method for concentrating a biological specimen comprising an analyte of interest for subsequent analysis. The method comprises the steps of: (a) applying a liquid suspension of one or more samples comprising the biological specimen and the analyte of interest to a matrix, wherein the liquid suspension of the one or more samples is applied in a first volume; (b) drying the matrix containing the liquid suspension; and (c) reconstituting the one or more samples with a controlled volume of a reconstitution fluid to produce a reconstituted sample, wherein the controlled volume of the reconstitution fluid is less than the first volume. The invention provides that the application and drying of the specimen can be performed for the benefit of separate reconstitution at another location, and conversely methods are also provided for reconstitution of a dried specimen which was previously prepared by separate individuals.
In another aspect; the present invention provides a method for pooling and concentrating a number of biological specimens from fluid samples in which at least one specimen comprises an analyte of interest for subsequent analysis. The method comprises the steps of: (a) applying a volume of a liquid suspension of a first biological specimen to a matrix, and drying the matrix containing the liquid suspension of the first biological specimen: (b) applying about the same volume of a liquid suspension of a second biological specimen to the matrix, and drying the matrix containing the liquid suspension of the second biological specimen: (c) repeating step (b) for applying and drying about the same volume of a liquid suspension of each biological specimen to be applied and dried on the same matrix; and (d) reconstituting the dried biological specimens on the matrix with less volume of reconstitution fluid than the total sum volumes of the liquid suspension of each biological specimen pooled to produce a reconstituted sample. In certain embodiments, the reconstituting volume is about the same volume as each individual volume of liquid suspension for each biological specimen applied to the matrix.
In a preferred embodiment, the method further provides a method for analyzing a testing volume of the reconstituted sample for the analyte of interest, wherein the testing volume is less than the volume of the reconstituted sample. In certain embodiments, the testing volume is about the same as the reconstituting volume divided by the number of pooled volumes of each liquid suspension for each biological specimen. By controlling the testing volume and the reconstituting volume, the concentration of the analyte present in the test sample is substantially equal to the concentration of the analyte in each of the original liquid suspensions for each biological specimen, when the analyte is present in only one of the biological specimens of the total pooled biological specimens. If the analyte is present in multiple biological specimens in the pool, the concentration of the analyte present in the test sample will be substantially equal to the sum of the analyte concentrations in each biological specimen in the pool.
In certain embodiments of the present disclosure, the reconstitution fluid comprises 1× phosphate buffered saline (PBS) or nuclease-free water optionally with the addition of sodium azide or other antimicrobial agent. The present invention encompasses any reconstituting buffers known or later discovered that are suitable for reconstituting dried biological samples for release from the matrix.
The invention provides a method of determining the presence of an analyte in a biological specimen comprising reconstituting on a matrix a controlled volume of a dried plurality of unique representative samples comprising a biological specimen, wherein the controlled volume is less than a combined volume of the representative samples applied to the matrix before being dried, and determining if the analyte is present in the reconstituted concentrated biological specimen. The present invention further provides subsequent analysis using the recovered concentrated biological specimen containing analytes of interest. In preferred embodiments, the analytes of interest are proteins, nucleic acids, or fragments thereof that are detected using analytical and diagnostic methods known in the art.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A is a perspective view of an assembled device according to one embodiment of the present invention.
FIG. 1B is a perspective view of a disassembled device according to one embodiment of the present invention ready for sample addition.
FIG. 2 illustrates addition of sample to the matrix of a device according to one embodiment of the present invention.
FIG. 3 illustrates loading a liquid suspension of a biological specimen containing analytes of interest on the top of the matrix and allowing the liquid suspension to fully absorb into the matrix.
FIG. 4 is a perspective view of preparing to transfer the matrix of a device according to one embodiment of the present invention into an empty syringe barrel.
FIG. 5 is a perspective view of completed delivery of the matrix into the syringe barrel.
FIG. 6 illustrates rehydration of the matrix by a pipette tip gently placed on the top of the matrix and slowly dispensing reconstitution buffer.
FIG. 7A illustrates insertion of the plunger into the syringe barrel.
FIG. 7B illustrates application of pressure to the syringe plunger.
FIG. 7C illustrates compression of the matrix plug.
FIG. 7D illustrates completion of sample recovery.



DETAILED DESCRIPTION OF THE INVENTION
The present invention may be understood more readily by reference to the following detailed description of the preferred embodiments of the invention and the Examples included herein. However, before the present devices, materials, and methods are disclosed and described, it is to be understood that this invention is not limited to specific embodiments of the devices, materials and methods, as such may, of course, vary, and the numerous modifications and variations therein will be apparent to those skilled in the art. It is also to be understood that the terminology used herein is for the purpose of describing specific embodiments only and is not intended to be limiting.
The present invention provides a device and method for collection, storage and transportation of a liquid suspension of a biological specimen containing an analyte of interest. More particularly, the present invention provides a device and method for collection, storage and transportation of a liquid suspension containing a biological specimen in a dry state that is convenient and simple to use. As used herein, the terms “a” or “an” mean one or more than one depending upon the context in which they are used. For example, “an analyte” in a sample refers to a particular type of analyte of interest (e.g. HIV DNA), of which there may be numerous copies within the sample. Where a sample is referred to as containing an analyte, it is understood that the sample may contain many other types of analytes of interest also.
As used herein, the phrase “collection, storage and transportation” refers to the preservation of liquid suspension of biological specimen containing analytes of interest in a form suitable for subsequent analysis. The time period for which biological specimen may be preserved according to the present invention may be as short as the time necessary to transfer a sample of biological specimen from a collection source to the place where subsequent analysis is to be performed. Therefore, the invention provides that such preservation can occur for a period of several minutes, hours, days, months or greater. The temperature conditions under which a biological specimen may be stored in the device provided by the present invention are not limited. Typically, samples are shipped and/or stored at ambient or room temperature, for example, from about 15° C. to about 40° C., preferably about 15° C. to 25° C. In another embodiment the samples may be stored in a cool environment. For example, in short-term storage, the samples can be refrigerated at about 2° C. to about 10° C. In yet another example, the samples may be refrigerated at about 4° C. to about 8° C. In another example, in long-term storage, the samples can be frozen at about −80° C. to about −10° C. In yet another example, the samples can be frozen from about −60° C. to about −20° C. In addition, the device may preferably but not necessarily be stored in dry or desiccated conditions or under an inert atmosphere.
In preferred embodiments, the present invention provides a device comprising a container defining an interior space having side walls, a bottom and a lid which may be opened. In one preferred embodiment, the invention provides a scalable container having a threaded screw cap. In other embodiments, the lid can remain attached to the container such as a flip-top fashion. In another embodiment, the lid may also be cork-like. The lid preferably provides an air-tight seal when the container is closed. The shape of the container is not limited, but can be cylindrical, rectangular, or tubular for example. Materials for construction of the container are not limited, but can be plastic, metal foil, laminate comprising metal foil, metallized film, glass, silicon oxide coated films, aluminum oxide coated films, liquid crystal polymer layers, and layers of nano-composites, metal or metal alloys, acrylic, and amorphous carbon for example.
In another embodiment, the lid may be scaled to the container by heating. Suitable seals include, but are not limited to, lap seals, fin seals, butt seals, and the like, and the seals can be made by any of the suitable means known to those skilled in the art such as heating sealing, or the application of cold or hot melt adhesives, a heated bar, hot air, infrared radiation, ultrasonic sealing, radio frequency sealing, laser sealing, and the like.
The device also comprises a matrix inside the container. The matrix has an ability to absorb a liquid suspension readily and quickly, as well as to release the biological specimen containing analytes of interest efficiently and precisely. In preferred embodiments, the matrix can absorb at least 0.1 ml, 0.2 ml, 0.3 ml, 0.4 ml, 0.5 ml, 0.6 ml, 0.7 ml, 0.8 ml, or 0.9 ml, 1.0 ml or preferably 5.0 ml or greater, sample of a liquid suspension of a biological specimen containing an analyte of interest. In other preferred embodiments the matrix can absorb at least 7.5 ml or at least 10.0 ml of a sample of a liquid suspension containing a biological specimen. The term “absorb” and “adsorb” are used interchangeably, and means that the liquid suspension is incorporated into or onto the matrix in such a way as to not be readily removed from the matrix unless subjected to conditions which are intentionally performed to remove the absorbed liquid suspension of biological specimen or the reconstituted biological sample from the matrix.
The volume of the matrix may or may not expand upon absorption of the liquid suspension, and may or may not contract upon drying. However, a liquid saturated matrix can be compressed by at least about 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, or 90% or more of its saturated volume, using manual pressure as applied to a barrel and syringe configuration as disclosed herein. Volumetric compression is one convenient technique for release of the reconstituted biological specimen, however, any other means, such as centrifugation, can alternatively be employed to release the biological specimen from the matrix.
Therefore, as used herein, the term “compress,” “compressable,” “compression,” and other derivatives of the word “compress” means that the volume of the saturated matrix is reduced as compared to the original volume of the saturated matrix while a force or a pressure is applied to the matrix. Compressibility is a function of the porosity of the matrix, and as such the matrix is porous to approximately the same extent as it is compressible, i.e., the matrix is least about 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, or 90% or more porous. As used herein, the term “a portion of the biological specimen” means at least some of the biological specimen contained in the liquid suspension is released from the matrix. In one preferred embodiment, the matrix is compressed until the maximum volume of the reconstituted biological specimen is released from the matrix.
In preferred embodiments, the matrix is three-dimensional in a shape such as cylinder, cube, sphere, pyramid or cone. In one of the preferred embodiments, the matrix is in the shape of a cylinder about 45 mm in length and 17 mm in diameter. However, the matrix can be widened, lengthened, or shortened to achieve any needed volume capacity. In yet another preferred embodiment, the matrix is removable from a container. As used herein, the term “removable” means that the matrix can be detached or separated from the container. In one of the preferred embodiments, the matrix is removably mounted in a holder on the lid of a container. In yet another preferred embodiment, the matrix is removably mounted to a lid extension of the transportation or storage container. In other embodiments, the matrix can be mounted in the container, and compressed therein to release reconstituted biological suspension through a port for example.
The matrix of the present invention includes any absorbent material to which the liquid suspension of biological specimen containing analytes of interest will absorb and which does not inhibit storage or subsequent analysis of the analytes of interest applied thereto. The material of the matrix itself preferably has no or minimal effect on the measurement or detection of the analytes of interest. In preferred embodiments, the matrix comprises an absorbent material that is of a porous nature to provide entrainment of the liquid suspension in the matrix. As used herein, the term “entrain” and derivatives thereof means that during storage the liquid suspension is bound to the matrix without substantial reliance on ionic, covalent or van der waals interactions. A matrix suitable for this purpose includes, but is not limited to, a matrix that is composed of cellulose acetate fibers, wood or cotton derived cellulose, nitrocellulose, carboxymethylcellulose, hydrophilic polymers including polypropylene, polyester, polyamide, carbohydrate polymers, polytetrafluoroethylene, glass fiber, nylon, and combinations thereof.
As used herein, the term “liquid suspension” refers to any liquid medium and mixture containing biological specimens. This includes, for example, water, saline; cell suspensions of humans, animals and plants: extracts or suspensions of bacteria, fungi, plasmids, viruses; extracts or suspensions of parasites including helminthes, protozoas, spirochetes; liquid extracts or homogenates of human or animal body tissues, blood, bone, liver, kidney, brain; media from DNA or RNA synthesis; mixtures of chemically or biochemically synthesized DNA or RNA, and any other sources in which any biological specimen is or can be in a liquid medium.
As used herein, the term “biological specimen” refers to samples, either in liquid or solid form, having dissolved, suspended, mixed or otherwise contained therein, any analytes of interest, for example, genetic material. As used herein, the term “genetic material” refers to nucleic acids that include either or both deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The term “biological specimen” also refers to whole blood, plasma, serum, lymph, synovial fluid, bone marrow, cerebrospinal cord fluid, semen, saliva, urine, feces, sputum, vaginal lavage, skin scrapings, hair root cells, or the like of humans or animals, physiological and pathological body liquids, such as secretions, excretions, exudates and transudates; any cells or cell components of humans, animals, plants, bacterials, fungi, plasmids, viruses, parasites, or the like that contain analytes of interest, and any combination thereof.
As used herein, the term “analytes of interest” refers to any micro- or macro-molecules in the biological specimen that are interested to be detected or analyzed. These include, for example, nucleic acids, polynucleotides, oligonucleotides, proteins, polypeptides, oligopeptides, enzymes, amino acids, receptors, carbohydrates, lipids, cells, any intra- or extra-cellular molecules and fragments, virus, viral molecules and fragments, antibodies and antibody fragments, antigens, prions, bacteria, parasites, and naturally occurring or synthetic chemicals, e.g. drugs, metals or the like.
In one of the preferred embodiments, the analytes of interest are nucleic acids including either or both DNA or RNA. As used herein, the term “nucleic acids” or “polynucleotide” refers to RNA or DNA that is linear or branched, single or double stranded, a hybrid, or a fragment thereof. The term also encompasses RNA/DNA hybrids. The term also encompasses coding regions as well as upstream or downstream noncoding regions. In addition, polynucleotides containing less common bases, such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine, and other are also encompassed. Other modifications, such as modification to the phosphodiester backbone, or the 2′-hydroxy in the ribose sugar group of the RNA are also included. The nucleic acids/polynucleotides may be produced by any means, including genomic preparations, cDNA preparations, in vitro synthesis, RT-PCR, and in vitro or in vivo transcription. In one preferred embodiment, the nucleic acids are either or both viral DNA or RNA, for example, DNA or RNA from human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), or any other human or animal viral pathogen. In another preferred embodiment, the analyte of interest comprises an antibody, such as an antibody for HIV, HBV or HCV. In yet another preferred embodiment, the analyte of interest are a parasite, such as the parasite Trypanosoma cruzi which is responsible for Chagas disease or parasites of the genus Plasmodium which are responsible for malaria, and identifying portions thereof.
Although most of the specific, examples described herein relate to biological specimens of human origin, the methods disclosed herein may be employed in the analysis of biological specimens procured from plants and animals as well. For example, the pooling and/or concentrating methods disclosed herein may be useful for testing livestock for virus and prion diseases. Further, the proposed tests may be used to pool and/or concentrate biological specimens in other fluids. For example, the methods may be employed to test for the presence of Salmonella and/or other bacteria or parasites in a water source. Moreover, the proposed tests may be used for concentration of blood for the detection of organisms that can cause sepsis, such as Staphylococcus aureus. 
In preferred embodiments, the device provided by the present invention also includes a desiccant, either a natural or synthetic desiccant, inside the container to create and maintain dry conditions within the container. Preferably, the matrix is dried to render the specimen biologically inactive with respect to proteases and nucleases before and during storage and transportation. Preferably, the desiccant is in vaporous communication with the matrix in the device having a dye indicator reactive with moisture whereby the desiccant changes to a bright color when exposed to humidity or moisture. In one of the preferred embodiments, the desiccant is in vaporous communication with the matrix so that an air permeable barrier is formed in-between the desiccant and the matrix inside the container. The desiccant used in the device is commonly known in the art, including but not limited to montmorillonite clay, lithium chloride, activated alumina, alkali alumino-silicate, DQ11 Briquettes, silica gel, molecular sieve, calcium sulfate, and calcium oxide. The desiccant can be provided with a colorimetric indicator of water content.
The matrix of the invention may optionally include a composition absorbed to the matrix wherein the composition protects against degradation of the analytes of interest contained in the biological specimens. As used herein, the term “protects against degradation of the analytes of interest” means that a matrix in the device of the invention maintains the stored analytes of interest contained in the biological specimens in a substantially nondegraded form, providing that the analytes of interest are suitable for many different types of subsequent analytical procedures. Protection against degradation may include protection against substantial damaging of analytes of interest caused by chemical or biological agents including action of bacteria, free radicals, nucleases, ultraviolet radiation, oxidizing agent, alkylating agents, or acidic agents (e.g., pollutants in the atmosphere). Preferably, the composition absorbed on the matrix of the invention may include one or more of a weak base, a chelating agent, a protein denaturing agent such as a detergent or surfactant, a nuclease inhibitor, and a free radical trap. In the case where the stored analyte of interest is RNA, particularly unstable RNA, the composition may include RNase inhibitors and inactivators, genetic probes, complementary DNA or RNA (or functionally equivalent compounds), proteins and organic moieties that stabilize RNA or prevent its degradation.
Another composition which protects against degradation which may be optionally used is an oxygen scavenger element. As used herein, the term “oxygen scavenging element” refers to is a substance that consumes, depletes or reduces the amount of oxygen from a given environment without negatively affecting the samples of interests. Suitable oxygen scavenging elements are well-known to those skilled in the art. Non-limiting examples of oxygen scavenging elements include but are not limited to compositions comprising metal particulates reactive with oxygen such as transition metals selected from the first, second or third transition series of the periodic table of the elements, and include manganese II or III, iron II or III, cobalt II or III, nickel II or III, copper I or II, rhodium II, III or IV, and ruthenium. The transition metal is preferably iron, nickel or copper. An example of an iron oxygen scavenging element is D500 from Multisorb. Other commercially available oxygen scavengers may also be purchased from companies such as Mitsubishi, Dow, or the like. Other examples of oxygen scavenging element may be enzymes which consumes, depletes or reduces the amount of oxygen from the given environment without negatively affecting the samples of interests.
In another embodiment, the container may optionally comprise a modified atmosphere such as nitrogen or argon through well known gas purging process prior to sealing, shipping, or storing. The term “modified atmosphere” refers to any replacing or altering normal atmospheric gas compositions with at least one inert gas or gas which does not degrade the sample of interests.
As used herein, a “weak base” suitable for the composition of the invention may be a Lewis base which has a pH of about 6 to 10, preferably about pH 8 to 9.5. The weak base suitable for the composition of the invention may, in conjunction with other components of the composition, provide a composition pH of 6 to 10, preferably, about pH 8.0 to 9.5. Suitable weak bases according to the invention include organic and inorganic bases. Suitable inorganic weak bases include, for example, an alkali metal carbonate, bicarbonate, phosphate or borate (e.g., sodium, lithium, or potassium carbonate). Suitable organic weak bases include, for example, tris-hydroxymethyl amino methane (Tris), ethanolamine, triethanolamine and glycine and alkaline salts of organic acids (e.g., trisodium citrate). A preferred organic weak base is a weak monovalent organic base, for example, Tris. The weak base may be either a free base or a salt, for example, a carbonate salt. It is believed that the weak base may provide a variety of functions, such as protecting the analytes of interest from degradation, providing a buffer system, ensuring proper action of the chelating agent in binding metal ions, and preventing the action of acid nucleases which may not be completely dependent on divalent metal ions for functioning.
As used herein, a “chelating agent” is any compound capable of complexing multivalent ions including Group II and Group III multivalent metal ions and transition metal ions (eg., Cu, Fe, Zn, Mn, etc). Preferably, the chelating agent is ethylene diamine tetraacetic acid (EDTA), citrate or oxalate. It is believed that one function of the chelating agent is to bind multivalent ions which if present with the stored biological specimen may cause damage to the analytes of interest, especially to nucleic acids. Ions which may be chelated by the chelating agent include multivalent active metal ions, for example, magnesium and calcium, and transition metal ions, for example, iron. Both calcium and magnesium are known to promote nucleic acid degradation by acting as co-factors for enzymes which may destroy nucleic acids (e.g., most known nucleases). In addition, transition metal ions, such as iron, may readily undergo oxidation and reduction and damage nucleic acids by the production of free radicals or by direct oxidation.
The composition can further include a protein denaturing agent if the analytes of interest are nucleic acids. As used herein, a “protein denaturing agent” functions to denature non-nucleic acids compounds, for example, nucleases. If the protein denaturing agent is a detergent or a surfactant, the surfactant may also act as a wetting agent to facilitate the uptake of a sample by the dry solid matrix. The terms “surfactant” and “detergent” are synonymous and may be used interchangeably throughout the specification. Any agent which denatures proteins without substantially affecting the nucleic acids of interest may be suitable for the invention. Preferred protein denaturing agents include detergents. As used herein “detergents” include ionic detergents, preferably anionic detergents. A preferred anionic detergent suitable for the invention may have a hydrocarbon moiety, such as an aliphatic or aromatic moiety, and one or more anionic groups. Particularly preferred anionic detergents include sodium dodecyl sulphate (SDS) and sodium lauryl sarcosinate (SLS). The ionic detergent causes inactivation of a microorganism which has protein or lipid in its outer membranes or capsids, for example, fungi, bacteria or viruses. This includes microorganisms which may be pathogenic to humans or which may cause degradation of nucleic acids. It is believed that inactivation of a microorganism by a detergent is a result of destruction of the secondary structure of the organisms external proteins, internal proteins, protein containing membranes, or any other protein necessary for viability. However, the detergent may not inactivate some forms of organisms, for example, highly resistant bacterial spores and extremely stable enteric virions.
The composition of the invention may optionally include a free radical trap. As used herein, a “free radical trap” is a compound which is sufficiently reactive to be preferred, over a DNA molecule or a component thereof, as a reactant with a free radical, and which is sufficiently stable not to generate damaging free radicals itself. Examples of a suitable free radical trap include: uric acid or a urate salt, mannitol, benzoate (Na, K, Li or tris salt), 1-3 dimethyl uric acid, guanidine, guanine, thymine, adenine, cytosine, in N-acetyl-histidine, histidine, deferoxamine, dimethyl sulfoxide, 5′5′ dimethyl pyrroline-N-oxide, thiocyanate salt and thiourea. Preferred free radical traps include mannitol, thiocyanate salts, uric acid or a urate salt. It is believed that the longer the period of time for which the nucleic acid is to be stored the more likely that a free radical trap may be advantageously included in the composition sorbed to the solid matrix. Even if the nucleic acid is only to be stored for a matter of minutes, a free radical trap may still be incorporated into the composition. It is believed that one function of the free radical trap may be to trap nucleic acid damaging free radicals. For example, when the free radical trap used is uric acid or urate salt it may be converted to allantoin which may also act as a free radical trap that preferentially accepts free radicals that would otherwise damage nucleotide bases, for example, guanine. Preferably, the free radical trap reacts with free radicals regardless of source (including free radicals present in the air). Free radicals may be generated through oxidation or reduction of iron in biological specimen, such as blood. Typically, free radicals are believed to be generated by spontaneous oxidation of the groups which are present, for example, in denatured serum protein of blood. Free radicals may also be generated by radiation such as UV light, x-rays and high-energy particles. In addition, free radical traps which are also a weak acid, e.g. uric acid, may also function as a component of the buffering system provided by the weak base discussed above. Also, the free radical trap may enhance removal of a stored sample of nucleic acids if in situ processing is not desired.
Referring to FIGS. 1A & 1B, an exemplary transportation or storage device of the invention is shown for collecting, storing and transporting liquid suspension of biological specimen containing analytes of interest is shown. The container 20 is cylindrical and has side walls 22, a bottom 24 and an openable lid 26, which sealingly engages the container 20 opening. The lid 26 has an extension 28 that holds a removable matrix 30 inside the container 20. The matrix 30 is a cylinder capable of absorbing 1 ml of a liquid suspension of a biological specimen and compress by at least 50% of the volume of the saturated matrix to release a portion of the biological specimen. Accordingly, a desiccant 40 is also placed inside the container 20, separated with the matrix 30 by an optional air permeable barrier 42, for in vaporous communication with the matrix 30 to control humidity or moisture therein.
The present invention further provides a method for collecting, storing or transporting a liquid suspension of biological specimen containing analytes of interest. The method includes: a) applying the liquid suspension of biological specimen to the matrix in the device, and b) scaling the lid/cap on the device after the liquid suspension applied thereon is dry. In preferred embodiments, the liquid suspension is air-dried at room temperature. Other commonly available drying methods, such as vacuum dry, low heat dry, low pressure dry, and fan dry, may also be used. In certain embodiments, the matrix is advantageously dried by an evaporative process rather than a pressure-driven filtration process to better preserve the integrity of the biological specimen and/or analyte of interest. The present invention provides that multiple liquid samples can be loaded onto the matrix by drying each loaded sample in successive, or selective, order.
Referring to FIG. 1B, the lid 26 of the container 20 has a lid extension 28 holding a removable matrix 30 which is disassembled. A liquid suspension of any biological specimen containing analytes of interest is added on the top of the matrix 30 and is allowed to fully absorb into the matrix 30 (See FIG. 3). The lid 26 with the matrix 30 having bound biological specimen thereon is allowed to air-dry, optionally additional biological sample is added to the matrix and dried, and then the matrix is reassembled with the container 20 for storage or transportation at ambient temperature.
The method of the present invention further optionally includes intermediate steps of applying a stabilizing composition to the matrix to protect the analytes of interest against degradation. Depending upon the analytes of interest, the stabilizing composition, as discussed above, may include but is not limit to one or more of a weak base, a chelating agent, a protein denaturing agent such as a detergent or surfactant, a nuclease inhibitor, and a free radical trap. Particularly for protection of unstable RNA, the stabilizing composition may include RNase inhibitors and inactivators, genetic probes, complementary DNA or RNA (or functionally equivalent compounds), proteins and organic moieties that stabilize RNA or prevent its degradation.
The present invention further provides a method for recovering from the matrix in the device the biological specimen containing analytes of interest. In preferred embodiments, the method includes the following steps: a) applying reconstitution buffer to the matrix at a volume less than the total volume of liquid biological specimen added to the matrix, to rehydrate and concentrate the bound biological specimen containing analytes of interest, and b) releasing from the matrix a portion of the reconstituted biological specimen. According to the present invention, the reconstitution buffer can include the components of 1× phosphate buffered saline (PBS) or nuclease-free water optionally with the addition of sodium azide or other antimicrobial agent. The reconstitution buffer may also include any number or combinations of available biological preservatives or blood anticoagulants including but not limited to ethylenediaminetetraacetic acid (EDTA), sodium citrate, and heparin. PBS or nuclease-free water serves as the sterile and neutral medium for the rehydration, resuspension, and recovery of the analyte(s) of interest from the matrix. When included, antimicrobial agents such as sodium azide prevent microbial growth and subsequent contamination with RNases. When included, biological preservatives such as EDTA, sodium citrate, and heparin serve as anticoagulants and/or chelating agents. The reconstitution buffer may also include any number or combinations of available detergents, such as SDS, for cell lysis.
In the embodiments shown in FIGS. 4-7, the biological sample is prepared for analysis. FIG. 4 is a perspective view of preparing to transfer the matrix 30 of the device an the empty syringe barrel 52. FIG. 5 is a perspective view of completed delivery of the matrix 30 into the syringe barrel 52.
FIG. 6 illustrates rehydration of the matrix 30 by a pipette tip 53 gently placed on the top of the matrix 30 and slowly dispensing a controlled volume of reconstitution buffer. FIG. 7A illustrates insertion of the plunger 54 into the syringe barrel 54. FIG. 7B illustrates application of pressure to the syringe plunger 42. FIG. 7C illustrates compression of the matrix 30. FIG. 7D illustrates completion of sample recovery from the matrix 30.
In one of the preferred embodiments, the analytes of interest are nucleic acids including either or both DNA or RNA molecules. Preferably, the liquid suspension of biological specimen contains at least about 500 ng isolated DNA or RNA molecules, more preferably at least about 1 μg DNA or RNA molecules. As used herein, the term “isolated,” “isolation,” and other derivatives of the word “isolate” means that the DNA or RNA molecules are substantially free from some of the other cellular material with which it is naturally associated, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized.
The present invention further provides that the analytes of interest contained in the biological specimen recovered from the matrix of the device into the reconstitution buffer are subject to subsequent analysis. As used herein, the term “subsequent analysis” includes any analysis which may be performed on recovered biological specimens stored in reconstitution buffer. Alternatively, the analytes of interest contained in the biological specimen may be isolated, purified or extracted prior to analysis using methods known in the art. The analytes of interest may be subjected to chemical, biochemical or biological analysis. In one of the preferred embodiments, the analytes of interest are nucleic acids including either or both DNA or RNA molecules that can be detected or analyzed with or without prior extraction, purification or isolation. DNA or RNA extraction, purification or isolation, if necessary, is performed based on methods known in the art. Examples of subsequent analysis include polymerase chain reaction (PCR), ligase chain reaction (LCR), reverse transcriptase initiated PCR, DNA or RNA hybridization techniques including restriction fragment length polymorphism (RFLP), viral DNA or RNA detection and quantification, viral load tests, DNA or RNA genotyping, etc. “Subsequent analysis” also includes other techniques using genetic probes, genomic sequencing, enzymatic assays, affinity labeling, methods of detection using labels or antibodies and other similar methods.
The present invention also provides a kit for collecting, storing and transporting a liquid suspension of biological specimen containing analytes of interest. The kit of the present invention provides a device disclosed herein including one or more containers, one or more matrixes, and desiccant and instructions for the use thereof to collect biological specimens. The kit may optionally include a stabilizing solution. Kits of the present invention can further include a reconstitution buffer, a compression device and further protocols for concentrated rehydration and recovery of the biological specimen. The container of the kit may be any container suitable for use during application of a liquid suspension of biological specimen containing analytes of interest to the matrix or during application and one or more phases of subsequent processing of a sample of the biological specimen. Therefore, a kit may be used to apply a liquid suspension to the matrix where the matrix is removed from the kit container for processing in a different container. Alternatively, a liquid suspension of biological specimen may be applied, stored, transported and further processed all in the same kit container.
The kit may also include one or more of any of the matrixes disclosed herein. This includes one or more matrix with or without compositions for protection of analytes of interest contained in the biological specimen. One aspect of the kit of the present invention is that the reconstituted biological specimen containing analytes of interest is released by compressing the matrix. In some embodiments, this procedure may avoid vortexing and centrifuging the sample, providing decreased chance of sample damage, human labor costs and matrix contamination of the sample. A compression device of the kit of the present invention may be any device that is used to provide a force or pressure on the matrix to compress it. In one of the preferred embodiments, the compression device is a syringe, wherein the matrix is placed in the syringe barrel and the force or pressure is applied to the plunger of the syringe to compress the matrix to release the reconstituted biological specimen.
It has been discovered that the invention may also be used to efficiently concentrate and analyze fluids containing biological specimens, such as blood resources. It is particularly useful for batch testing a pool of unique fluid samples in accordance with methods of the present invention. In one method of the present invention, a representative sample may be taken from each of a plurality of unique fluid samples. The term “representative sample” generally refers to a volume portion of a fluid containing a biological specimen. The representative samples may be applied onto the matrix and allowed to fully absorbed into the matrix. For example, the representative samples may be collected in a container, such as a pipette, and then applied to the matrix. Alternatively, the representative samples may be added sequentially to the matrix while providing sufficient time to allow each representative sample to fully absorb into the matrix, and also may be dried on the matrix between successive, or selective, applications. Each of the representative samples may be provided in substantially equal volume.
The matrix may be then dried and inserted in the container for storage and transportation. The matrix may be allowed to air dry or it may be force dried as described previously. The representative samples may then be reconstituted with a controlled volume of a reconstitution buffer. The term “controlled volume” generally refers to a measured, predetermined volume of reconstitution buffer to be added to the matrix to reconstitute or rehydrate the sample. In preferred embodiments, the controlled volume of the reconstitution fluid is less than the combined volume of the representative samples. For example, the controlled volume used for reconstitution may be the same as the volume of a single representative sample pooled within the matrix. As such, the biological specimens and/or analytes of interest present in the representative samples may be concentrated upon rehydration. A testing volume may then be taken from the reconstituted pooled sample for subsequent analysis. The term “reconstituted pooled sample” generally refers to a liquid suspension of the representative samples added to the matrix after reconstitution buffer is added to the matrix. The term “testing volume” generally refers to measured, predetermined volume of reconstituted pooled sample which is to be analyzed. In preferred embodiments of the present invention, the testing volume may be less than the volume of the reconstituted pooled sample. For example, in sonic embodiments, the testing volume may be about 50 μl to about 500 μl, or more preferably about 200 μl to about 250 μl.
In an embodiment of the present invention, the testing volume taken is substantially equal to the reconstituted volume of the representative samples divided by the pooled volume of the representative samples. The “pooled volume” is equal to the quantity of representative samples pooled in the matrix multiplied by the volume of each representative sample. In other words, the term “pooled volume” refers the total volume of the representative samples applied to the matrix in combination or sequentially. Using such an approach, the amount of analyte present in the testing volume is approximately commensurate with the amount of analyte present in the contributed sample of the pooled volume. In sonic embodiments, the amount of reconstitution buffer used to rehydrate the samples may be commensurate in volume to the volume of one of the representative samples. By controlling the volume of reconstitution fluid, the concentration of the analyte present in the test sample will be substantially equal to the concentration of the analyte in one of the representative samples, assuming that the analyte is present in only one sample in the batch. If the analyte is present in multiple samples in the pool, the concentration of the analyte present in the test sample will be substantially equal to the sum of the analyte concentrations in each sample in the pool.
The present invention thus provides an effective and efficient method of concentrating a batch of representative samples for subsequent analysis. Surprisingly, it has been discovered that such a method may be used to prepare test samples which possess analyte in ideal concentrations and loads for analysis. If the 1:1 ratio of sample volume to reconstitution volume is maintained, the concentrated test sample may be analyzed using a threshold concentration test with substantially the same sensitivity as if the representative sample itself were tested alone. Further, if the volume of the test sample taken from the reconstituted pooled sample is substantially equal to the volume of the reconstituted pooled sample divided by the pooled volume of the representative samples, the test volume will have a load equivalent to 1 ml of sample volume or pooled sample volume.
The foregoing method is particularly effective for efficiently analyzing or testing blood resources (e.g., blood, plasma, blood cells, platelets and other blood components) for pathogens and other conditions which render a particular blood resource unsuitable for use in a transfusion procedure. In one embodiment, a 1 ml representative sample may be procured from each of a plurality of blood plasma resources at a storage site (e.g., a blood bank or clinic). The representative samples of blood plasma may then be combined onto a matrix and allowed to fully absorb into the matrix. The matrix may then be allowed to dry and inserted into a container for storage and or transportation. The pooled plasma sample, being contained within the matrix inside the container, may be transported off-site or to an on-site laboratory for rehydration and analysis. In the laboratory, a 1 ml volume of reconstitution buffer may then be slowly added to the matrix to produce a reconstituted pooled sample. The reconstituted pooled sample may be extracted from the matrix, and a testing sample may then be procured from the reconstituted pooled sample for subsequent analysis. In preferred embodiments, the volume of the testing sample may be the inverse of the quantity of plasma samples pooled in the matrix in milliliters. For example, if 10 plasma samples were pooled in the matrix, 0.10 ml of the reconstituted plasma may be used as a test sample.
Such a method allows for the efficient concentration of each sample in the pool and overcomes many obstacles which have precluded the widespread use of biological concentrate analysis. Specifically, it has been found that use of the matrix in such a method allows for fast and cost-effective concentration of biological specimens without significant degradation of the biological specimen and analyte.
The foregoing procedure may also be used to concentrate a non-pooled sample. For example, 5 ml of a sample having a concentration of an analyte of interest at 1 mg/ml may be absorbed onto the matrix and allowed to dry. The sample may then be rehydrated with 1 ml of reconstitution buffer. This reconstituted sample would have a 5 fold increase in concentration of the analyte of interest compared to the original sample prior to dehydration.
The ability to efficiently concentrate a pooled batch of samples or non-pooled sample for subsequent analysis is important because there is a threshold of detection for any analyte being tested. If, for example, the threshold of detection for HIV requires a concentration of 100 virions per ml of plasma and the test sample has 400 virions per ml, the presence of HIV in the sample would be detected if the sample were tested by itself. If the sample is combined with 4 other samples, the concentration of HIV in the pool would be diluted to only 80 virions per ml. If the pooled sample were tested, the test result would be negative (a false negative) because the concentration of the HIV is below the threshold of detection. The method of the present invention, however, concentrates the reconstituted pooled sample such that the HIV would be present in the reconstituted pooled sample at the original concentration of 400 virions per ml. As such, an HIV positive test result would be produced from analysis of a test volume taken from the reconstituted pooled sample.
It should now be appreciated that any number of samples may be combined onto a common matrix to efficiently analyze the batch using the foregoing method. Various considerations may dictate the optimal quantity of samples to pool onto a common matrix. For example, the volume of the representative sample needed for evaluation, the absorbent capacity of the matrix, and the total quantity of samples to be evaluated are all relevant considerations. Furthermore, since a test result indicating the presence of a pathogen in the sample pool generally will not indicate which sample within the pool produced the test result, in some cases it will be more efficient to test smaller batches.
Throughout this application, various publications are referenced. The disclosures of all of these publications and those references cited within those publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.
It should also be understood that the foregoing relates to preferred embodiments of the present invention and that numerous changes may be made therein without departing from the scope of the invention. The invention is further illustrated by the following examples, which are not to be construed in any way as imposing limitations upon the scope thereof. On the contrary, it is to be clearly understood that resort may be had to various other embodiments, modifications, and equivalents thereof, which, after reading the description herein, may suggest themselves to those skilled in the art without departing from the spirit of the present invention and/or the scope of the appended claims.
EXAMPLES
Example 1
One (1.0) ml Sample Preparation and Device Recovery Kit
Kit Components:
This example provides a kit for the preparation, transportation, and recovery of thirty-six (36) dr biological specimens from bodily fluids or tissue. Materials and reagents for the preparation and recovery of thirty-six (36) one (1.0) ml samples for dried ambient transportation include the following:














Component
Quantity









Device Kit containers (tubes)
36 each



Reconstitution Buffer
3 × 13 ml



Disposable 3 ml Syringes
36 each



15 ml Conical Centrifuge Tubes
36 each










Storage and Handling:

Upon receipt, all kit components are stored dry at room temperature (15-25° C.). Only use device container tubes when the indicating desiccant is blue in color. The device kit container tubes should not be if the indicating desiccant appears white or pink in color. Materials, such as 1000 μl pipette, 1000 μl sterile DNase-free, Rnase-free pipette tips with aerosol barrier, rack for holding 15 ml conical tubes, safety glasses, laboratory coat, powder-free disposable gloves and biohazard waste container, are also required but are not provided by the kit.
Safety Precautions:
Disposable powder-free gloves are used to handle all materials as though capable of transmitting infectious agents. Utilize good laboratory practices and universal precautions relating to the prevention of transmission of blood borne pathogens (See Centers for Disease Control. Update: Universal precautions for prevention of transmission of human immunodeficiency virus, hepatitis B virus and other blood borne pathogens in healthcare settings. MMWR, 1988; 37:377-82, 387-8; National Committee for Clinical Laborator Standards. Protection of laboratory workers from infectious disease transmitted by blood, body fluids, and tissue; approved guideline. NCCLS Document M29-A Villanova (PA): NCCLS; 1997 December 90p; Federal Occupational Safety and Health Administration. Bloodborne Pathogens Standard, 29 CFR 1910, 1030). Immediately, clean up any spills suspected of potentially containing infectious agents with 0.5% w/v sodium hypochlorite (10% v/v bleach). Dispose of all specimens and materials coming into contact with specimens as though they contain infectious agents. In the event that materials known or suspected of containing infectious agents are ingested or come in contact with open lacerations, lesions, or mucous membranes (eyes, nasal passages, etc.), consult a physician immediately.
Example 2
Sample Preparation Using the Device Kit
The sample preparation steps were performed within a biological safety cabinet using sterile technique and universal precautions relating to the handling of potentially infectious materials. Before beginning the sample preparation process, the protocol of using the device kit that is illustrated in FIGS. 1A & 1B should be familiarized.
Before loading a sample liquid suspension of biological specimen containing analytes of interest, the cap from the device container was unscrewed, inverted and placed on a clean working surface with the absorbent matrix facing upwards (See FIGS. 1A & 1B). About up to 1 ml of sample fluid was slowly added to the top of the matrix plug and allowed it to fully absorb into the matrix. The device kit matrix loaded with the sample fluid was allowed to air-dry. In general, air-drying within a biological safety cabinet takes approximately 4.5 to 5 hours. Once the sample is completely dry, the cap holding the dried specimen-containing matrix was carefully reattached back to the device kit container tube. The specimen is now ready for shipment or storage at ambient temperature.
Example 3
Sample Recovery Using the Device kit
The sample recovery steps were also performed within a biological safety cabinet using sterile technique and universal precautions relating to the handling of potentially infectious materials. Basically, a sterile 3 or 5 ml disposable Luer-LokTM syringe (provided by the kit) was inserted into a 15 ml collection tube (also provided by the kit). The plunger was removed from the syringe barrel. The absorbent matrix containing the dried specimen was transferred into the syringe barrel by pressing the matrix against the sterile inside of the syringe barrels mouth with just enough pressure to break it free from the attached cap and allow it to fall freely to the bottom of the syringe (See FIGS. 4 & 5). The syringe barrel with detached matrix plug was placed into a 15 ml conical collection tube, which is further placed into a rack. About 0.1 ml of Reconstitution Buffer (supplied by the kit) was applied slowly and directly to the top of the matrix plug to gently re-hydrate the dried specimen absorbed inside the matrix (See FIG. 6). It is necessary to inspect the absorption rate and adjust the application speed as needed while adding the reconstitution buffer, and try not to allow buffer to collect at the bottom of the syringe without first being absorbed into the matrix because failing to fully absorb the reconstitution buffer may result in lower recovery yields. The re-hydrating specimen was allowed to incubate for at least 10 minutes at room temperature prior to adding an additional 175 μl of Reconstitution Buffer to the top of the matrix plug.
The syringe plunger was re-inserted into the syringe barrel and depressed with firm even pressure until the plunger has completely compressed the matrix plug and a maximum volume of approximately 1 ml is collected inside the 15 ml collection tube (See FIGS. 7A, 7B, 7C, & 7D). The syringe barrel, the plunger and the compressed matrix plug were then removed from the 15 ml collection tube and discarded into an appropriate waste receptacle. The 15 ml collection tube containing the newly recovered specimen was sealed with the provided screw cap. The reconstituted sample is ready for storage, testing, or further subsequent analysis.
Example 4
TRUGENE HIV-1 Genotyping Assays Using Reconstituted Sample from the Device Kit
The device kit collection performance characteristics were examined, compared, and established with highly characterized samples using clonal analysis and polymorphic fingerprinting tools. For example, HIV Genotyping results were obtained using RNAs extracted from a 1 ml volume of reconstituted plasma from a device kit stored for 1 day and 7 days, respective. All extractions were performed using the QIAGEN QIAamp Viral RNA Mini Kit, known in the art. All genotyping assays were performed using the BAYER TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System, also known in the art. The device kit HIV Genotyping results were compared with that obtained from frozen plasma, and the summary of genotyping results for both HIV and HIV/HCV coinfected samples were shown in Tables 1(A), 1(B), 1(C), 2(A), 2(B), and 2(C).







TABLE 1(A)







TRUGENE HIV-1 (MT1-SC2-R0001, 100,000 HIV copies/ml)











Frozen Plasma
Device Kit Day 1
Device Kit day 7





Protease





Region


109
S37N*
S37N*
S37N*


121
R41K*
R41K*
R41K*


178
D60E*
D60E*
D60E*


184
I62V*
I62V*
I62V*


187
L63P#
L63P#
L63P#


214
I72M*
I72M*
I72M*


229
V77I*
V77I*
V77I*


Reverse


Transcriptase


Region


247
R83K*
R83K*
R83K*


361
D121A*
D121A*
D121A*


367
D123E*
D123E*
D123E*


403
I135V*
I135V*
I135V*


604
I202V*
I202V*
I202V*





*represents polymorphism:


#represents resistance mutation













TABLE 1(B)







TRUGENE HIV-1 (MT1-AS2-R0001, 64,700 HIV copies/ml)











Frozen Plasma
Device Kit Day 1
Device Kit day 7














Protease





Region


 28
L10I#
L10I#
L10I#


 37
I13V*
I13V*
I13V*


 94
V32I#
V32I#
V32I#


 97
L33F#
L33F#
L33F#


109
S37N*
S37N*
S37N*


136
M46L#
M46L#
M46L#


160
I54V#
I54V#
I54V#


187
L63P#
L63P#
L63P#


211
A71V#
A71V#
A71V#


229
V77I*
V77I*
V77I*


244
V82A#
V82A#
V82A#


268
L90M#
L90M#
L90M#


Reverse


Transcriptase


Region


121
M41L#
M41L#
M41L#


127
K43E*
K43E*
K43E*


130
E44D#
E44D#
E44D#


199
D67N#
D67N#
D67N#


205
T69D#
T69D#
T69D#


247
R83K*
R83K*
R83K*


352
V118I#
V118I#
V118I#


367
D123N*
D123N*
D123N*


412
E138G*
E138G*
E138G*


586
G196E*
G196E*
G196E*


628
L210W#
L210W#
L210W#


640
L214F*
L214F*
L214F*


643
T215Y#
T215Y#
T215Y#


709
D237E*
D237E*
D237E*





*represents polymorphism;


#represents resistance mutation













TABLE 1(C)







TRUGENE HIV-1 (MT1-GL1-R0001, 24,792 HIV copies/ml)











Frozen Plasma
Device Kit Day 1
Device Kit day 7














Protease





Region


 28
L10I#
L10I#
L10I#


 31
V11L*
V11L*
V11L*


 37
I13V*
I13V*
I13V*


 40
K14N*
K14N*
K14N*


 97
L33F#
L33F#
L33F#


109
S37N*
S37N*
S37N*


160
I54M#
I54M#
I54M#


184
I62I/V*
I62I/V*
I62I/V*


187
L63P#
L63P#
L63P#


211
A71V#
A71V#
A71V#


217
G73S#
G73S#
G73S#


229
V77I/V*
V77I/V*
V77I/V*


250
I84V#
I84V#
I84V#


265
L89V*
L89V*
L89V*


268
L90M#
L90M#
L90M#


Reverse


Transcriptase


Region


121
M41L#
M41L#
M41L#


127
K43Q*
K43Q*
K43Q*


220
L74V#
L74V#
L74V#


364
E122K/E*
E122K/E*
E122K/E*


367
D123E/D*
D123E/D*
D123E/D*


403
I135T*
I135T*
I135T*


484
S162H*
S162H*
S162H*


529
D177D/G*
D177D/G*
D177D/G*


532
I178I/M*
I178I/M*
I178I/M*


550
M184V#
M184V#
M184V#


628
L210W#
L210W#
L210W#


631
R211K*
R211K*
R211K*


640
L214F*
L214F*
L214F*


643
T215Y*
T215Y*
T215Y*


682
L228H#
L228H#
L228H#





*represents polymorphism;


#represents resistance mutation
















TABLE 2(A)









TRUGENE HIV-1
HIV-1 GeneTanker













Sample

Sample



Frozen
Tanker
Frozen
Tanker



Plasma
day 7
Plasma
day 7















Protease






Region


 43
I15V*
I15V*
I15V*
I15V*


103
E35E/D*
E35D*
E35D*
E35D*


106
M36I/L#
M36I#
M36I#
M36I#


109
S37N/S*
S37N*
S37N*
S37N*


169
R57K*
R57K*
R57K*
R57K*


184
162I/V*
162I/V*
I62V*
I62V*


187
L63A++
L63A++
L63A++
L63A++


Reverse


Transcriptase


Region


190
K64R*
K64R*
K64R*
K64R*


364
E122K/E*
E122K/E*
E122K/E*
E122K/E*


403
I135T*
I135T*
I135T*
I135T*


631
R211K*
R211K/R*
R211K*
R211K*


640
L214F*
L214F*
L214F*
L214F*


733
V245E*
V245E*
X
X





*represents polymorphism;


#represents resistance mutation;


++represents unexpected mutation
















TABLE 2(B)









TruGene HIV-1
HIV-1 GeneTanker












Frozen
Sample
Frozen
Sample



Plasma
Tanker day 7
Plasma
Tanker day 7















Protease






Region


103
E35D*
E35D*
E35D*
E35D*


109
S37N*
S37N*
S37N*
S37N*


229
V77I/V*
V77I/V*
V77I/V*
V77I/V*


Reverse


Transcriptase


Region


301
K101K/E#
K101K/E#
K101K/E#
K101K/E#


316
V106A/V#
V106A/V#
V106A/V#
V106A/V#


364
E122K*
E122K*
E122K*
E122K*


631
R211K*
R211K*
R211K*
R211K*


640
L214F*
L214F*
L214F*
L214F*


643
T215Y#
T215Y#
T215Y#
T215Y#


733
V245K*
V245K*
X
X





*represents polymorphism;


#represents resistance mutation
















TABLE 2(C)









TruGene HIV-1
HIV-1 GeneTanker













Sample

Sample



Frozen
Tanker
Frozen
Tanker



Plasma
day 7
Plasma
day 7





Protease






Region


 43
I15V*
I15V*
I15V*
I15V*


103
E35D*
E35D*
E35D*
E35D*


106
M36I#
M36I#
M36I#
M36I#


109
S37D*
S37D*
S37D*
S37D*


169
R57K/R*
R57K*
R57K*
R57K*


Reverse


Transcriptase


Region


121
M41L#
M41L#
M41L#
M41L#


127
K43K/T*
K43K/T*
K43K/T*
K43N*


130
E44E/D#
E44E/D#
E44E/D#
E44D#


199
D67N#
D67N#
D67N#
D67N#


367
D123N*
D123N*
D123N*
D123N*


586
X
G196E/G*
X
G196E/G*


619
Q207E*
Q207E*
Q207E*
Q207E*


628
L210W#
L210W#
L210W#
L210W#


631
R211K*
R211K*
R211K*
R211K*


640
L214F*
L214F*
L214F*
L214F*


643
T215Y#
T215Y#
T215Y#
T215Y#





*represents polymorphism;


#represents resistance mutation






The data in Tables 1(A), 1(B), 1(C), 2(A), 2(B), and 2(C) indicate that the reconstituted samples from device kit stored at ambient temperature for 1 and 7 days prior to testing showed no subsequent degradation of peak intensity or increased signal to noise ratio. The reconstituted samples from device kit showed a high degree of correlation and reproducibility to that of standard frozen plasma samples.
Example 5
BAYER VERSANT HIV-1 RNA 3.0 Assay (bDNA) Using Reconstituted Samples from the Device Kit
In this study, the reconstituted samples from device kit collection were stored dry at ambient temperature for 1 day prior to testing. The Bayer Versant HIV-1 RNA 3.0 Assay is known in the art. The data shown in Table 3 indicate the reproducibility using samples from the device kit.












TABLE 3






RNA
RNA
Mean RNA
Log10
Mean Log10


Description
copies/ml
Log10
Log10
Variance
Variance*




















Device Kit
43,480
4.64
4.58
0.06
0.03


Device Kit
34,285
4.54
4.58
0.04
0.03


Device Kit
39,085
4.59
4.58
0.01
0.03


Device Kit
37,751
4.58
4.58
0
0.03


Device Kit
35,298
4.55
4.58
0.03
0.03


Device Kit
40,005
4.6
4.58
0.02
0.03


Device Kit
5,439
3.74
3.76
0.02
0.04


Device Kit
5,295
3.72
3.76
0.04
0.04


Device Kit
5,150
3.71
3.76
0.05
0.04


Device Kit
6,142
3.79
3.76
0.03
0.04


Device Kit
6,611
3.82
3.76
0.06
0.04


Device Kit
5,905
3.77
3.76
0.01
0.04


Device Kit
726
2.86
2.75
0.11
0.07


Device Kit
522
2.72
2.75
0.03
0.07


Device Kit
710
2.85
2.75
0.1
0.07


Device Kit
417
2.62
2.75
0.13
0.07


Device Kit
568
2.75
2.75
0
0.07


Device Kit
476
2.68
2.75
0.07
0.07









Example 6
Roche UltraSensitive AMPLICOR HIV-1 MONITOR Test, Version 1.5 for Quantifying Viral Load Using Reconstituted Samples from the Device Kit
In this study, the reconstituted samples from the device kit collection were stored dry at ambient temperature for 7 days prior to testing. The Roche UltraSensitive AMPLICOR HIV-1 MONITOR Test v1.5 is known in the art and was performed using samples reconstituted from the device kit dried EDTA plasma. The data shown in Table 4 indicate the reproducibility using samples from the device kit.












TABLE 4










LOG10



Copies/

LOG10
LOG10
Mean


Sample Type
ml
LOG10
Mean
Variance
Variance




















Dried EDTA Plasma
3,861
3.59
3.6
0.01
0.01


Dried EDTA Plasma
4,060
3.61
3.6
0.01
0.01


Dried EDTA Plasma
4,085
3.61
3.6
0.01
0.01


Dried EDTA Plasma
14,640
4.17
4.04
0.13
0.09


Dried EDTA Plasma
9,314
3.97
4.04
0.07
0.09


Dried EDTA Plasma
9,249
3.97
4.04
0.07
0.09


Dried EDTA Plasma
19,981
4.3
4.28
0.02
0.03


Dried EDTA Plasma
19,816
4.3
4.28
0.02
0.03


Dried EDTA Plasma
16,788
4.23
4.28
0.05
0.03


Dried EDTA Plasma
21,757
4.34
4.44
0.1
0.09


Dried EDTA Plasma
25,155
4.4
4.44
0.04
0.09


Dried EDTA Plasma
37,087
4.57
4.44
0.13
0.09


Dried EDTA Plasma
1,275
3.11
3.19
0.08
0.05


Dried EDTA Plasma
1,837
3.26
3.19
0.07
0.05


Dried EDTA Plasma
1,590
3.2
3.19
0.01
0.05


Dried EDTA Plasma
1,037
3.02
3.04
0.02
0.05


Dried EDTA Plasma
981
2.99
3.04
0.05
0.05


Dried EDTA Plasma
1,274
3.11
3.04
0.07
0.05





OVERALL LOG10 Mean Variance = 0.05


Device Kit specimens were stored dry at ambient temperature for 7 days prior to testing.


N = 18 (6 samples × 3 replicates each)






Example 7
TRUGENE HCV 5′NC Genotyping Assays Using Reconstituted Samples from the Device Kit
In this study, the HCV 4′NC genotypes were obtained from RNA extracted from 140 μl of a 1.0 ml volume of thawed or reconstituted plasma. RNA was extracted using the QIAGEN QIAamp Viral RNA Mini Kit, known in the art. All genotyping assays were performed using the BAYER TRUGENE HCV 5′NC Genotyping Kit and OpenGene DNA Sequencing System, also known in the art. The device kit HCV 5′NC Genotyping results were compared with that obtained from frozen plasma, and the summary of genotyping results for HIV/HCV coinfected samples is shown in Tables 5(A), 5(B), and 5(C).







TABLE 5 (A)







Co-Infected Sample #1










From Frozen Plasma
Filter Matrix d7 Post Prep







Genotype: 2b
Genotype: 2b

















TABLE 5 (B)







Co-Infected Sample #1










From Frozen Plasma
Filter Matrix d7 Post Prep







Genotype: 3
Genotype: 3a

















TABLE 5 (C)







Co-Infected Sample #1










From Frozen Plasma
Filter Matrix d7 Post Prep







Genotype: 1a
Genotype: 1a










Example 8
Comparison of Viral Load and Resistance Genotyping Between Frozen Plasma and a Novel Dried Plasma Transportation Medium (Device Kit) on Treated Patient Samples
Methods:
Viral load, RNA extraction, and genotyping: HIV-1 viral loads were determined using either the Standard or UltraSensitive AMPLICOR HIV-1 MONITOR® Test v1.5 (Roche Diagnostics, Indianapolis, Ind.), VERSANT® HIV-1 RNA 3.0 Assay (bDNA) (Bayer Healthcare, Tarrytown, N.Y.) or NucliSens® HIV-1 QT Assay (bioMerieux, Durham, N.C.). Total viral RNA for all samples used in genotyping were extracted using the QIAamp® Viral RNA Mini Kit (Qiagen, Valencia, Calif.). HIV-1 genotype was determined using either or both the TRUGENE® HIV-1 Genotyping Kit (Bayer Healthcare) and the HIV-1 GeneTanker Genotyping Complete Assay (Research Think Tank, Inc). The HCV genotype was determined using the TRUGENE HCV 5′NC Genotyping Kit (Bayer Healthcare). All sequencing, data processing and reporting were performed using the OpenGene® DNA Sequencing System (Bayer Healthcare).
The device matrix (FIGS. 1A and 1B) has a maximum capacity of 1 ml. A 1 ml volume of plasma was added to each matrix, allowed to air-dry in a biosafety cabinet for 4-5 hours, then packaged in the device kit tube and stored or shipped at ambient temperature. Dried sample matrices were re-hydrated with the appropriate volume of Reconstitution Buffer to recover 1 ml of reconstituted plasma.
Amplicor viral load intra-assay reproducibility using the device kit: three matrices were prepared for each of six randomly selected HIV-1 positive plasma samples (N=18). The matrix specimens were reconstituted and recovered on day 7 post preparation and were used to examine the intra-assay viral load reproducibility of the UltraSensitive AMPLICOR viral load assay.
Versant viral load intra-assay reproducibility using the device kit: six matrices were prepared for each of three serial dilutions from an HIV-1 positive sample (N=18). The matrix specimens were reconstituted and recovered on day 1 post preparation and were used to examine the intra-assay viral load reproducibility of the Versant viral load assay.
NucliSens viral load intra-assay reproducibility using the device kit: five matrices were prepared for each of three randomly selected HIV-1 positive plasma samples (N=15).
The matrix specimens were reconstituted and recovered on day 3.5 post preparation and were used to examine the intra-assay viral load reproducibility of the NucliSens viral load assay.
HIV-1 genotyping stability: Three archived HIV-1 positive plasma samples with previously determined viral-loads were randomly selected to prepare the device matrices for genotype stability testing. Two identical sets of matrices were prepared for each sample following the method described above. The dry packaged matrices were stored at ambient temperature for up to 7 days. Reconstituted plasma for each set of matrices was recovered on either day 1 or day 7, respectively. For each sample the entire recovered volume was extracted. Genotyping was performed on all samples using the TRUGENE HIV-1 genotyping kit, following the manufacturer's protocol. The matrix genotypes were then compared with previously determined frozen plasma-derived genotypes.
HIV-1/HCV co-infection: For each of three HIV-1/HCV co-infected plasma samples, a single matrix and frozen plasma aliquot were prepared by an external laboratory and shipped overnight to Research Think Tank. The plasma aliquots were shipped on dry ice, while the device kit specimens were shipped separately at ambient temperature. Upon receipt, the matrix specimens were stored at ambient temperature until reconstituted for testing on day 7 post preparation. The corresponding frozen plasma were thawed for testing in parallel on day 7. All samples were assayed for viral load in duplicate using the Standard AMPLICOR viral load assay. A 140 μL volume of each sample was extracted for total RNA (HIV-1 and HCV), then genotyped using the TRUGENE HIV-1, the HIV-1 GeneTanker and the HCV TRUGENE HCV 5′NC kits, following manufacturer's protocol.
Phenotyping: RNA extracted from matched The device kit and frozen plasma HIV-1/HCV co-infected specimens were submitted for PhenoscriptTM (VIRalliance, Paris, France) phenotyping analysis.
Results:
Device Kit Characteristics: The device kit consisted of an absorbent fibrous matrix for the preparation of dried plasma specimens and a desiccant storage/transportation tube. The matrix yielded an approximate recovered plasma volume of 1.035+/−0.03 ml. The device kit specimens were dried in a biosafety cabinet, at ambient temperature, for a minimum of 4.5 hours prior to packaging. Viral load assays: The mean log10 difference between matched frozen and the device kit dried plasma specimens using the standard AMPLICOR HIV-1 and VERSANT HIV-1 assay was 0.36 and 0.51, respectively (Table 6A and B; Standard Roche viral load for 9 randomly selected specimens and Bayer bDNA HIV-1 viral load for 12 randomly selected specimens respectively). Intra-assay quantitative reproducibility experiments for device kit indicated an overall Log10 mean variance of 0.05 for the UltraSensitive AMPLICOR HIV-1 assay at day 7 (Table 4), 0.05 for the VERSANT HIV-1 assay at day 1 (Table 3) and 0.06 for the NucliSens HIV-1 QT assay at day 3.5 (Table 7). Viral load values obtained from the device kit specimens were consistently lower than those obtained from matched frozen plasma specimens.
Genotyping assays: The sequence quality generated between matched the device kit and frozen plasma specimens was comparable. However, in several sequences the device kit specimens exhibited an increase in sequence quality (data not shown). Mutation profiles obtained using either the TRUGENE HIV-1 and/or HIV-1 GeneTanker genotyping kits exhibited a high degree of concordance between matched the device kit and frozen plasma specimens (Table 1 and 2). This concordance was consistent regardless of HIV-1 viral-load, storage time or shipping conditions prior to genotype testing. Among matched co-infected the device kit and frozen plasma specimens, there was a 100% concordance at the genotype level for HCV using the TRUGENE HCV 5′NC kit. While samples 37 and 39 were in agreement at the subtype level, HCV subtype was unable to be determined for the sample 38 plasma specimens.
Phenotyping: Phenotype results were successfully obtained for all matched HIV-1/HCV co-infected The device kit and frozen plasma specimens.











TABLE 6 A







RNA

Log10


Sample
Description
Copies/ml
RNA Log10
Difference



















1
Plasma
23.15
4.3
0.4



Device Kit
7.87
3.9


2
Plasma
544.25
5.7
0.3



Device Kit
231.24
5.3


3
Plasma
33.17
4.5
0.2



Device Kit
20.36
4.3


4
Plasma
4.10
3.6
0.2



Device Kit
2.49
3.4


5
Plasma
394.70
5.6
0.5



Device Kit
106.41
5.0


6
Plasma
130.54
5.1
0.3



Device Kit
54.63
4.7


7
Plasma
11.28
4.0
0.2



Device Kit
6.53
3.8


8
Plasma
601.85
5.7
0.1



Device Kit
397.27
5.6


9
Plasma
4.73
3.6
0.6



Device Kit
1.15
3.0




















TABLE 6 B







RNA

Log10


Sample
Description
Copies/ml
RNA Log10
Difference



















1
Plasma
18.20
4.2
0.5



Device Kit
4.88
3.6


1
Plasma
49.22
4.6
0.4



Device Kit
16.55
4.2


1
Plasma
<7
NA
NA



Device Kit
<7
NA


1
Plasma
<7
NA
NA



Device Kit
<7
NA


1
Plasma
<7
NA
NA



Device Kit
<7
NA


1
Plasma
458.60
5.6
0.3



Device Kit
224.34
5.3


1
Plasma
41
2.6
0.6



Device Kit
10
2.0


1
Plasma
26.11
4.4
0.5



Device Kit
7.86
3.9


1
Plasma
40.85
4.6
0.5



Device Kit
12.05
4.0


1
Plasma
2.08
3.3
0.7



Device Kit
37
2.5


2
Plasma
225.36
5.3
0.4



Device Kit
88.64
4.9


2
Plasma
32.48
4.5
0.4



Device Kit
11.19
4.0





















TABLE 7







RNA
RNA
Mean RNA
Mean Log10


Sample
Description
Copies/m
Log10
Log10
Variance*




















3
Device Kit
87
2.9
2.8
0.0



Device Kit
64
2.8



Device Kit
52
2.7



Device Kit
59
2.7



Device Kit
81
2.9



Device Kit


3
Device Kit
16.70
4.2
4.2
0.0



Device Kit
21.50
4.3



Device Kit
19.05
4.2



Device Kit
19.55
4.2



Device Kit
22.37
4.3



Device Kit


3
Device Kit
130.00
5.1
5.0
0.0



Device Kit
110.50
5.0



Device Kit
95.00
4.9



Device Kit
120.00
5.0



Device Kit
138.00
5.1









Example 9
Pooling and Concentrating Biological Specimens
In this example, variations of a method of pooling, concentrating, and analyzing a plurality of unique fluid samples for an analyte of interest in accordance with the present invention are considered. In this example, five theoretical test runs are examined in Table 8—Run A, Run B, Run C, Run D, and Run E. In each run, one sample contains an analyte of interest and the other samples in the batch contain none of the analyte of interest. In each run, reconstitution buffer is provided in a volume commensurate with the volume of a single sample pooled in the matrix. Also, in each run, a test volume is taken from reconstituted pooled sample that is equal to the total reconstituted pooled volume divided by the original pooled volume.













TABLE 8







A
B
C
D
E























Pool
Qsample
#
5
10
7
5
5



Vsample
ml
1.00
2.00
2.00
1.00
1.50



manalyte
mg
1.00
3.00
1.00
2.00
1.00



Csample
mg/ml
1.00
1.50
0.50
2.00
0.67



Cpool
mg/ml
0.20
0.15
0.07
0.40
0.13


Test
Vrecons
ml
1.00
2.00
2.00
1.00
1.50



Crecons
mg/ml
1.00
1.50
0.50
2.00
0.67



Ctest
mg/ml
1.00
1.50
0.50
2.00
0.67



Vtest
ml
0.20
0.10
0.14
0.20
0.20



manalyte
mg
0.20
0.15
0.07
0.40
0.13









In Run A, 5 representative samples are procured from unique fluids. Each representative sample has a volume of 1.00 ml. The mass of the analyte of interest present in one representative sample is 1.00 mg (a concentration in the sample of 1.00 mg/ml). The representative samples are then combined onto a matrix and allowed to fully absorb into the matrix. When pooled in the matrix, the analyte is diluted by the other representative samples and is present in a concentration of 0.20 mg/ml. The matrix is allowed to dry between each sample volume, or after the sample volumes have been added to the matrix.
Reconstitution buffer is added at a volume of 1.00 ml to the matrix. The reconstituted pooled sample is separated from the matrix. The analyte is present in the reconstituted pooled sample at a concentration of 1.00 mg/ml. A test volume of 0.20 ml is taken from the reconstituted pool sample for analysis. The analyte is present in the test volume at a concentration of 1.00 mg/ml, the same as in the reconstituted pooled sample. As such, the analyte is present in the test volume at a mass of 0.20 mg.
In Run B, 10 representative samples are procured from unique fluids. Each representative sample has a volume of 2.00 ml. The mass of the analyte of interest present in one representative sample is 3.00 mg (a concentration in the sample of 1.50 mg/ml). The representative samples are then combined onto a matrix and allowed to fully absorb into the matrix. When pooled in the matrix, the analyte is diluted by the other representative samples and is present in a concentration of 0.15 mg/ml. The matrix is then allowed to dry.
Reconstitution buffer is added at a volume of 2.00 ml to the matrix. The reconstituted pooled sample is separated from the matrix. The analyte is present in the reconstituted pooled sample at a concentration of 1.50 mg/ml. A test volume of 0.10 ml is taken from the reconstituted pool sample for analysis. The analyte is present in the test volume at a concentration of 1.50 mg/ml, the same as in the reconstituted pooled sample. As such, the analyte is present in the test volume at a mass of 0.15 mg.
In Run C, 7 representative samples are procured from unique fluids. Each representative sample has a volume of 2.00 ml. The mass of the analyte of interest present in one representative sample is 1.00 mg (a concentration in the sample of 0.50 mg/ml). The representative samples are then combined onto a matrix and allowed to fully absorb into the matrix. When pooled in the matrix, the analyte is diluted by the other representative samples and is present in a concentration of 0.07 mg/ml. The matrix is then allowed to dry.
Reconstitution buffer is added at a volume of 2.00 ml to the matrix. The reconstituted pooled sample is separated from the matrix. The analyte is present in the reconstituted pooled sample at a concentration of 0.50 mg/ml. A test volume of 0.14 ml is taken from the reconstituted pool sample for analysis. The analyte is present in the test volume at a concentration of 0.50 mg/ml, the same as in the reconstituted pooled sample. As such, the analyte is present in the test volume at a mass of 0.07 mg.
In Run D, 5 representative samples are procured from unique fluids. Each representative sample has a volume of 1.00 ml. The mass of the analyte of interest present in one representative sample is 2.00 mg (a concentration in the sample of 2.00 mg/ml). The representative samples are then combined onto a matrix and allowed to fully absorb into the matrix. When pooled in the matrix, the analyte is diluted by the other representative samples and is present in a concentration of 0.40 mg/ml. The matrix is then allowed to dry.
Reconstitution buffer is added at a volume of 1.00 ml to the matrix. The reconstituted pooled sample is separated from the matrix. The analyte is present in the reconstituted pooled sample at a concentration of 2.00 mg/ml. A test volume of 0.20 ml is taken from the reconstituted pool sample for analysis. The analyte is present in the test volume at a concentration of 2,00 mg/ml, the same as in the reconstituted pooled sample. As such, the analyte is present in the test volume at a mass of 0.40 mg.
In Run E, 5 representative samples are procured from unique fluids. Each representative sample has a volume of 1.50 ml. The mass of the analyte of interest present in one representative sample is 1.00 mg (a concentration in the sample of 0.67 mg/ml). The representative samples are then combined onto a matrix and allowed to fully absorb into the matrix. When pooled in the matrix, the analyte is diluted by the other representative samples and is present in a concentration of 0.13 mg/ml. The matrix is then allowed to dry.
Reconstitution buffer is added at a volume of 1.50 ml to the matrix. The reconstituted pooled sample is separated from the matrix. The analyte is present in the reconstituted pooled sample at a concentration of 0.67 mg/ml. A test volume of 0.20 ml is taken from the reconstituted pool sample for analysis. The analyte is present in the test volume at a concentration of 0.67 mg/ml, the same as in the reconstituted pooled sample. As such, the analyte is present in the test volume at a mass 0.13 mg.
In each run, it should be noted that the analyte is present in the test volume in the same concentration as the representative sample containing the analyte. Further, the mass load of the analyte in the test volume is the same as in 1 ml of pooled sample prior to drying and reconstitution.
In this example, it is assumed that 100% of the analvte that is added to the matrix is recovered from the matrix during the steps of reconstituting the biological specimen and separating the biological specimen and analyte from the matrix. In some cases, less than 100% recovery may be expected. Several factors may affect the actual recovery from the matrix including the degradability of the analyte of interest and the characteristics of the matrix. Such a loss of analyte may be easily accounted for by experimentally determining a process efficiency for the analyte and matrix. If the loss is significant, less reconstitution fluid or larger sample volumes may be used to yield a more concentrated testing volume.
Example 10
Sample Concentrating and Pooling Adding 1 ml Sample and Reconstituting with 1 ml Buffer
The biological specimen (either from a single source to concentration or from multiple sources to demonstrate pooling and concentration) is applied to the matrix ViveST (from ViveBio, Norcross, Ga.) and allowed to dry before adding additional sample volume to that the same matrix in succession. When plasma ( ̃90% water) or blood ( ̃80% water) is added to the matrix the water will evaporate while the analytes including proteins, nucleic acids, etc., remain absorbed to the filter. Once the matrix is dry (either by air drying in a flow hood or drying aided by heat, for example) the sample can be transported and stored. Sample is rehydrated using 1 ml of reconstitution buffer (water, PBS, etc). Therefore, the analyte concentration is realized by the reduction of reconstitution buffer compared to the amount of water evaporated from the biological sample. This allows for large volumes of biological sample to be concentrated which may be required for pooling samples such as for the case in blood bank pooled sample testing or to increase sensitivity of the ability to detect low amounts of bacteria in the blood from septic patients.
In this example, the matrixes of six ViveST devices were loaded with 1 ml human plasma and allowed to dry in a flow hood for 8 hours. Additional 500 μL plasma was added to four of the matrixes, and allowed to dry, and additional 500 μL plasma was added to two of the matrixes. Therefore, in total there were 2 each of the dried plasma containing 1 ml, 1.5 ml, or 2 ml. Each of the matrixes was placed into a luer lock syringe with the barrel removed and resuspended with 1 ml 1× PBS and allowed to reconstitute. Sample was collected by compressing the plunger within the syringe barrel. Protein concentrations were determined using a Nanodrop 2000 spectrophotometer (|mg/ml|=A280 ×path length 1 mm) and presented in Table 9.












TABLE 9







Plasma

Run




Added
Reconstitution
1 mg/ml
Run 2 mg/ml









  1 ml
1 ml
420
420



1.5 ml
1 ml
540
560



2.0 ml
1 ml
733
734










Results show increases in protein concentrations correlating to the increase in plasma added to the matrix. These data indicate there is concentration of analytes (in this case, as measured by proteins) retained by the matrix when increased sample volume is added in succession to a single matrix.
In another example, the matrixes in eight ViveST devices were loaded with 1 ml human plasma and allowed to dry in a flow hood for 8 hours. Additional 500 μL plasma was added to six of the matrixes, and allowed to dry. Additional 250 μL plasma was added to the remaining matrixes until in total there were 2 matrixes each containing the dried plasma from 1 ml, 1.5 ml, 2 ml, or 2.5 ml. Each of the matrixes was placed into a luer lock syringe with the barrel removed and resuspended with 1 ml PBS and allowed to reconstitute. Sample was collected by compressing the plunger within the syringe barrel. Protein concentrations were determined (after a 1:10 dilution of the samples in molecular grade water) using a Nanodrop 2000 spectrophotometer (|mg/ml|=A280×path length 1 mm) and presented in Table 10.












TABLE 10







Plasma

Run




Added
Reconstitution
1 mg/ml
Run 2 mg/ml









  1 ml
1 ml
54
54



1.5 ml
1 ml
75
78



  2 ml
1 ml
87
88



2.5 ml
1 ml
94
96










Results show increases in protein concentrations correlating to the increase in plasma added to the matrix. The data indicate there is concentration of analytes (in this case, as measured by proteins) retained by the matrix when increased sample volume is added in succession to a single matrix.
In another example, the matrixes of ten ViveST devices were loaded with 1 ml human plasma and allowed to dry in a flow hood for 8 hours. Additional 500 plasma was added to eight of the matrixes, and allowed to dry. Additional 250 μL plasma was added until in total there were 2 each of the following dried plasma: 1 ml, 1.5 ml, 2.25 ml, 2.5 ml, 2.75 ml. Each of the matrixes was placed into a luer lock syringe with the barrel removed and resuspended with 600 μL lysis buffer and allowed to reconstitute. Sample was collected by compressing the plunger within the syringe barrel. Protein concentrations were determined (after a 1:10 dilution of the samples in molecular grade water) using a Nanodrop 2000 spectrophotometer (|mg/ml|=A280×path length 1 mm). Samples were then extracted using a genomic DNA extraction kit (DNA Ultraclean, MoBio Laboratories) and nucleic acid concentrations were determined using the Nanodrop and presented in Table 11.











TABLE 11





Plasma Added
Reconstitution
Run 1 mg/ml
Run 2 mg/ml
NA ng/μL



















  1 ml
600 μL
67
67
2


 1.5 ml
600 μL
108
108
1


2.25 ml
600 μL
143
151
3


 2.5 ml
600 μL
153
150
11


2.75 ml
600 μL
158
159
12









Results show increases in protein concentrations correlating to the increase in plasma added to the matrix. The data indicate there is concentration of analytes (in this case, as measured by proteins) retained by the matrix when increased sample volume is added in succession to a single matrix. Normally plasma has no cellular genomic DNA, however, some nucleic acids can be found either in the form of cell-free DNA or RNA. There is a slight increase in the nucleic acid concentrations as additional plasma was added supporting the concentration effect of multiple sample additions and water evaporation from the plasma to increase testing sensitivity of analytes.
Sample elutions were then combined with 10× gel loading dye (Invitrogen) and electrophoresis was carried out using a 1% agarose gel at 120 volts for 60 minutes. The bromophenol blue in the loading dye binds to proteins. The results (data not shown) indicate a gradient of the dye correlating both to the protein concentrations and the increase in plasma applied to the matrix. The lanes that contained the extracted sample elutions showed no bromophenol blue staining as expected (most proteins were removed during the extraction process).
Results show increases in protein concentrations correlating to the increase in plasma added to the matrix. The data indicate there is concentration of analytes (in this case, as measured by proteins) retained by the matrix when increased sample volume is added in succession to a single matrix.
Example 11
Sample Concentrating and Pooling 1 ml Sample and Reconstituting with <1 ml Buffer
In the following example, the biological specimen (either from a single patient to demonstrate concentration or from multiple patients to demonstrate pooling and concentration) is applied to the matrixes of ViveST and allowed to dry. When a biological sample, such as plasma ( ̃90% water) or blood ( ̃80% water), is added to the matrix the water will evaporate while the analytes, including proteins, nucleic acids, etc., remain absorbed to the matrix. Once the matrix is dry (such as either by air drying in a flow hood or drying aided by heat) the sample can be transported, stored, etc. Sample is rehydrated using <1 ml of reconstitution buffer (water, PBS). Concentration is realized by the reduction of reconstitution buffer compared to the amount of water evaporated from the original biological specimen.
In this example, pooled human plasma (1 ml) was applied to each matrix and allowed to dry in a biological flow hood overnight. The reconstitution of the analytes from the specimen on the matrix was performed using either 1 ml or 0.5 ml 1× PBS. Reconstitution for each reconstitution volume was repeated five times each. A control consisted of the same pooled human plasma in a frozen state and was processed in triplicate. HIV viral load testing was completed using the reconstituted product obtained from each of the total 13 matrixes. The results were as follows: Average HIV RNA copies/ml for the frozen control, elution using 1.75 ml, elution using 0.5 ml were 43,667, 38,400 and 50,100, respectively. The average log10 for the frozen control, elution using 1.175 ml, elution using 0.5 ml were 4.64, 4.54, 4.70, respectively (See Table 12 below).














TABLE 12












Std









Deviation



Rep
vRNA
Avg
Std Deviation
LOG10
Avg
log10


Description
No.
copies/ml
copies/ml
copies/ml
copies/ml
LOG10
copies/ml






















Frozen
1
48,300


4.68




Plasma


Control



2
41,900


4.62



3
40,800
43,667
4,050
4.61
4.64
0.04


Dried
1
13,300


4.12


Plasma


ViveST


Reconstitution
2
42,800


4.63


1.175 ml



3
49,500


4.69



4
47,200


4.67



5
39,200
38,400
14,583
4.59
4.54
0.24


Dried
1
56,900


4.76


Plasma


ViveST


Reconstitution
2
50,700


4.71


0.5 ml



3
46,400


4.67



4
50,900


4.71



5
45,600
50,100
4,505
4.66
4.70
0.04









The results show an increase detection of viral load in the samples where the reconstitution was decreased from 1.175 ml or 0.5 ml. These data indicates that the invention can effectively act as a concentration device for the plasma (or portion of that plasma) that when eluted with a smaller volume allows for accurate detection of low amounts of nucleic acid.
In another example, the matrixes of eight ViveST devices were loaded with 1 ml human plasma and allowed to dry in a flow hood for 8 hours. Each of the matrixes was placed in a syringe and resuspended in parts with either 1 ml, 750 μL, 500 μL, or 250 μL 1× PBS and allowed to reconstitute. Sample was collected by plunging the syringe. Protein concentrations were determined using a Nanodrop 2000 spectrophotometer (|mg/ml|=A280×path length 1 mm) and presented in Table 13.












TABLE 13







Plasma

Run




Added
Reconstitution
1 mg/ml
Run 2 mg/ml









1 ml
  1 ml
471
479



1 ml
.75 ml
549
543



1 ml
.50 ml
544
564



1 ml
.25 ml
809
815










Results show increases in protein concentrations correlating to the decrease in reconstitution buffer added to the matrix. The data indicate there is concentration of analytes (in this case, as measured by proteins) by the matrix due to reduced volume of reconstitution buffer, which still allows for absorbed analytes to elute, hence, increasing analyte:buffer ratio and testing sensitivity.
In another example, the matrixes of 4 ViveST devices were loaded with 1 ml human plasma and allowed to dry in a flow hood for 8 hours. Each of the matrixes was placed in a syringe and resuspended with either 1 ml or 250 μL 1× PBS and allowed to reconstitute. Sample was collected by plunging the syringe. Frozen plasma was used as a control. Samples were then extracted using a commercial DNA extraction kit (DNA Ultraclean, MoBio Laboratories) and nucleic acid concentrations were determined using the Nanodrop 2000 and presented in Table 14.












TABLE 14







Plasma

Run




Added
Reconstitution
1 ug/μL
Run 2 ug/μL









Frozen Plasma
none
4
3



1 ml
  1 ml
3
4



1 ml
.25 ml
7
5










Results show increases in nucleic concentrations correlating to the decrease in reconstitution buffer added to the matrix. Normally plasma has no cellular genomic DNA, however, some nucleic acids can be found either in the form of cell-free DNA or RNA. The data indicate there is concentration of analytes (in this case, as measured by nucleic acids) by the matrix due to reduced volume of reconstitution buffer, which still allows for absorbed analytes to elute, hence, increasing analyte:buffer ratio and testing sensitivity.

## Claims

1. A method of concentrating representative samples of a plurality of unique fluid samples comprising:
(a) combining the representative samples of the plurality of unique fluid samples on an absorbent matrix by successively applying the representative samples of the plurality of unique fluid samples onto the absorbent matrix, thereby forming a matrix containing the representative samples, wherein each of the representative samples is obtained from a different one of the plurality of unique fluid samples and comprises a biological specimen;
(b) drying the matrix containing the representative samples so that the representative samples on the matrix are in a dry state; and
(c) reconstituting the representative samples on the matrix in the dry state with a controlled volume of a reconstitution fluid, thereby forming reconstituted representative samples, wherein the controlled volume of the reconstitution fluid is less than a combined volume of the representative samples applied to the matrix.

2. The method of claim 1, wherein the controlled volume is substantially, equal to the volume of one of the representative samples.

3. The method of claim 1, further comprising analyzing a testing volume of the reconstituted representative samples for an analyte of interest, wherein the testing volume is less than the volume of the reconstituted representative samples, wherein the analyte of interest is present in the testing volume in a concentration commensurate with a concentration of the analyte of interest in one of the plurality of unique fluid samples.

4. The method of claim 3, wherein the testing volume is substantially equal to the controlled volume divided by the combined volume of the representative samples.

5. The method of claim 3, wherein said analyte of interest is selected from the group consisting of nucleic acids, proteins, carbohydrates, lipids, whole cells, cellular fragments, whole viruses and viral fragments, antibodies and antibody fragments, prions, bacteria, and parasites.

6. The method of claim 3, wherein said analyte of interest is a nucleic acid comprising DNA or RNA.

7. The method of claim 1, further comprising providing a container, the container having an interior space, a side wall, a bottom and an openable lid, and wherein the matrix is located inside the container and is removable from the container, wherein the matrix is porous and is configured to absorb a volume of at least 1 ml of a liquid suspension; and wherein the container further comprises a desiccant inside the container in vaporous communication with said matrix to maintain the biological specimen in a biologically inactive state.

8. The method of claim 7, wherein said matrix is removably mounted in a holder on the lid.

9. The method of claim 1, wherein the unique fluid samples are from the same individual.

10. The method of claim 1, wherein the unique fluid samples are pooled from a plurality of individuals.

11. The method of claim 1, wherein the matrix is configured to absorb at least 5 ml of a liquid suspension comprising the biological specimen.

12. The method of claim 1, wherein the matrix is configured to be compressed to at least 25% of the volume of said matrix to release a portion of the biological specimen.

13. The method of claim 1, wherein the matrix is configured to be compressed to at least 10% of the volume of said matrix to release a portion of the biological specimen.

14. The method of claim 1, further comprising drying the matrix after each application of the representative samples to the matrix.

15. The method of claim 1, wherein said biological specimen is selected from the group consisting of whole blood, plasma, serum, lymph, synovial fluid, urine, saliva, sputum, semen, vaginal lavage, bone marrow cerebrospinal cord fluid, a physiological body liquid, a pathological body liquid, and a combination thereof.

16. A method for concentrating a first biological specimen and a second biological specimen of a plurality of unique biological specimens for subsequent analysis of an analyte of interest, said method comprising:
(a) applying a first volume of a liquid suspension of a first biological specimen of the plurality of unique biological specimens to a matrix, thereby forming a matrix containing the liquid suspension of the first biological specimen;
(b) drying the matrix containing the liquid suspension of the first biological specimen so that the first biological specimen on the matrix is in a dry state;
(c) applying a second volume of a liquid suspension of a second biological specimen of the plurality of unique biological specimens to the matrix containing the first biological specimen in the dry state, thereby forming a matrix containing the first biological specimen and the liquid suspension of the second biological specimen, wherein the second volume is substantially equal to the first volume:
(d) drying the matrix containing the first biological specimen and the liquid suspension of the second biological specimen so that the first biological specimen and the second biological specimen on the matrix are in a dry state;
(e) reconstituting the first biological specimen and the second biological specimen of the plurality of unique biological specimens on the matrix with a controlled volume of a reconstitution fluid, thereby producing a reconstituted sample, wherein the controlled volume of the reconstitution fluid is less than a combined volume of liquid suspensions of the plurality of unique biological specimens applied to the matrix.

17. The method of claim 16, further comprising analyzing a testing volume of the reconstituted sample for the analyte of interest, wherein the testing volume is less than the volume of the reconstituted sample.

18. The method of claim 16, wherein the reconstitution fluid comprises 1×phosphate buffered saline (PBS) or nuclease-free water optionally with the addition of sodium azide or an antimicrobial agent.

19. The method of claim 16, wherein the plurality of unique biological specimens is pooled from a plurality of individuals.