Classifications

• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
  • G01N33/56983—Viruses

Definitions

• swab specimens 100 are used almost exclusively to deliver sample into solution 110 for the rapid test 120.
• Processing and testing the sample in the physician's office and other non- laboratory sample collection sites does not contemplate a means for enabling lab-based testing such as confirmatory and/or reflex testing or other tests the require lab-based analysis.
• a physician or other administrator of a POC rapid test
• a lab-based test using the sample collected at the site (e.g. the physician's office). Therefore, an opportunity to perform lab-based testing on such samples is lost.
• Swab samples 130 collected at POC sites within a hospital or clinic are almost exclusively placed within a volume of liquid transport media 140 for transfer to the testing laboratory for remote testing.
• the diluted samples 150 may be further processed by adding them to a solution 160 for a rapid test 170.
• this method often results in a POC sample diluted 5 to 10-fold, or more, which can diminish performance of the rapid test due to sample dilution effects.
• Collection and transport of a second swab at the POC site could be used to address the need to perform laboratory-based testing, although this is clearly not the standard of practice and doubles the number of samples to be taken.
• variations in collection methods, organism load, etc. could lead to erroneous results when comparing the test results between two independently collected swab specimens. Accordingly, a system and method that addresses these problems is desired.
• the various embodiments of the present invention enable linkage between POC rapid tests (e.g. immunoassays such as a test for flu virus) and laboratory-based testing
• the sample (which is any sample that is suspected of containing a target microorganism) is collected and processed under optimal conditions for the particular POC test utilized, ensuring the best possible clinical performance for the POC test (also referred to as a rapid test herein) .
• the sample can be a biological sample collected from a patient and can include any biological fluid or tissue sample including, but not limited to, blood, urine, saliva, and tissue scraped or swabbed from a patient. Samples can also include environmental samples collected in the conventional manner of wiping or swabbing a surface suspected of having the contaminating microorganism.
• Environmental samples can also include soil samples, air samples, water samples, food samples, etc.
• the sample is processed by combining it with a processing reagent compatible with the rapid test.
• the portion of the sample not used for the rapid test has heretofore been typically discarded.
• the remainder of the processed sample is then preserved to allow transfer to a laboratory-based testing environment where confirmatory testing, such as nucleic acid-based testing, can be performed.
• the remainder is not further diluted, but is still subjected to a laboratory-test .
• the site of sample collection and rapid test is referred to as local or POC, while the site for laboratory-based testing is referred to as remote.
• remote simply means removed from the site of sample collection and rapid testing. Remote could vary from very close distances such as different locations in the same building to much larger distances.
• Rapid immunoassays for use at a POC site are well known and commercially available. They are not described in detail herein.
• rapid immunoassays are known to detect a wide array of infectious diseases from patient sample including but not limited to influenza testing (e.g. H1N1) , RSV testing, Chlamydia trachomatis testing, Neisseria gonorrhea testing, etc.
• influenza testing e.g. H1N1
• RSV testing Chlamydia trachomatis testing
• Neisseria gonorrhea testing etc.
• samples are collected and first processed directly for use in a rapid immunoassay.
• the processing step utilizes a rapid test processing reagent and is optimized for producing the maximum clinical performance for the particular immunoassay to be used. This typically involves a relatively gentle lysis treatment in the presence of various salts and detergents. Such lysis reagents are well known and used in conjunction with the commercially available rapid immunoassays and are not described in detail herein. One skilled in the art is aware of the need to select a rapid test processing reagent that will not degrade the sample and make it unsuitable for a contemplated laboratory test .
• a portion of the processed sample is then delivered to the POC test device to generate a rapid diagnostic test result.
• the remainder (or a portion thereof) of the sample is preserved for transfer to a laboratory-based test environment for testing such as confirmatory testing using a molecular diagnostic method.
• the molecular diagnostic test is nucleic acid-based.
• the nucleic acid-based diagnostic test is PCR.
• stabilization transport diluents are utilized to increase stability of the sample.
• Various formulations are possible where possible constituents include but are not limited to buffers, salts, chelating agents, enzyme inhibitors, nucleic acid binding proteins, chaotropes, etc.
• constituents include but are not limited to buffers, salts, chelating agents, enzyme inhibitors, nucleic acid binding proteins, chaotropes, etc.
• One skilled in the art is aware of the suitable constituents and conditions
• the stabilization transport diluent for a particular application.
• the target microorganism in a sample is susceptible to being degraded by a chaotrope, then the skilled person would know not to include chaotropes in the stabilization transport diluent.
• the remainder of the processed sample not used for the rapid test may be added to the stabilization transport diluent.
• the stabilization transport diluent may already be present in the rapid test processing reagent used for the POC test.
• the stabilization transport diluent may be added to the remainder of the processed sample after a portion of the sample has been removed and used for the rapid immunoassay.
• the stabilization transfer diluent stabilizes nucleic acids in the sample.
• FIG. 1A illustrates the prior art method for the standard protocol for POC and lab-based testing.
• FIG. IB illustrates the method for POC and lab- based testing of the present invention.
• FIG. 2A/B demonstrates the results from RT-PCR for Influenza A from samples processed for POC testing under various dilution conditions.
• FIG. 3 demonstrates the results from RT-PCR for Influenza A from samples processed for POC testing using two different rapid test processing reagents and various storage conditions using the method of the present invention.
• FIG. 4 demonstrates the results from RT-PCR for Influenza A from samples processed for POC testing and then mixed with two different stabilization transport diluents and various storage conditions using the method of the present invention .
• FIG. 5 demonstrates the results from RT-PCR for Influenza A from samples processed for POC testing and then mixed with a stabilization transport diluent and various storage conditions using the method of the present invention.
• FIG. 6A-C demonstrate the results from RT-PCR for two strains of Influenza A and one strain of Influenza B under various storage conditions using the method of the present invention.
• FIG. 1A illustrates the current standard protocol for POC and lab-based testing.
• a specimen 105 is collected, for example, using a swab 100.
• Other conventional implements for collecting biological samples are contemplated for use herein. Such implements, such as a scraper or spatula are not described in detail herein and are well known to those skilled in the art.
• Specimen 105 is then processed directly by placing swab 100 with sample 105 in solution 110 for POC rapid testing 120. In this situation, any remaining sample is discarded and a new sample must be collected for additional lab-based testing such as confirmatory testing or reflex testing.
• specimen 105 on swab 130 is first diluted in transport media 140.
• a portion of the diluted transport media 140 containing specimen 105 is further processed in solution 160 for POC testing 170.
• processed specimen 105 is diluted to a level that diminishes the results of POC testing 170 as illustrated in Example 1 below.
• the remaining portion in the diluent is used for laboratory testing 150, such as subtyping and reflex testing.
• FIGS. IB illustrates one embodiment of the method for POC and laboratory testing of the present invention.
• Specimen 205 is collected on swab 200 and processed directly using a rapid test processing reagent 210 that is optimized for producing the maximum clinical performance for the particular immunoassay.
• the swab 200 is removed and the rapid test container 215 is closed with dispenser lid 216.
• the capped test container 215 with dispenser lid 216 is used to dispense a portion of processed sample 211 onto rapid test strip 220.
• Rapid POC testing 220 is performed using a portion of the specimen 211 processed in the rapid test processing reagent.
• the remaining portion 212 of the processed sample after POC testing is transported 300 to the clinical lab for laboratory testing 400.
• the remaining portion 212 of the processed sample after POC testing is added to transport vial 230 that contains stabilization transport diluent 240.
• the stabilization transport diluent is designed to help maintain the integrity of the sample.
• various formulations are possible depending upon a variety of factors including the stability of the target microorganism, the type of laboratory test contemplated, and the constituents of the rapid test reagent. Considering these factors, the skilled person will select conditions (e.g. optimal pH conditions) and constituents (e.g. buffer types, salts, chelating agents, enzyme inhibitors, nucleic acid binding proteins, chaotropes, etc.) for the stabilization transport diluent.
• the stabilized sample is then transported to the clinical lab 300 for confirmatory or other laboratory testing 400.
• This embodiment illustrates how one sample, specimen 205, can be processed at the POC site for both POC testing and lab-based testing. This embodiment also demonstrates that a sample processed in conditions optimal for POC testing can be used for lab-based testing.
• the rapid test processing reagent tris buffer, NaCl , 6% detergent and pH adjusted to 8.0
• the immunoassay testing results on the various sample dilutions are shown in Table 1.
• Samples diluted greater than 1:5 resulted in a negative rapid immunoassay test.
• specimen dilution should therefore be minimized or avoided.
• Dilution of the specimen (excluding the initial placement of the sample into solution) greater than 1:5 diminishes the possibility of detection with a rapid immunoassay test.
• the use of direct swab processing in the POC setting enhances the clinical performance of rapid immunoassays.
• standard POC testing methods using direct swab samples do not enable lab-based testing because of initial placement of such samples into a transport diluent.
• Figures 2A and 2B demonstrate that samples processed for rapid immunoassay testing could also be used for RNA extraction, which enabled lab-based PCR testing to be performed.
• RNA was extracted from samples diluted well below the limit of detection for the rapid test, indicating that even small amounts of viral RNA remained stable in the processed sample. Storage of the processed samples at 4°C or room temperature for up to four hours before RNA extraction also indicates the viral nucleic acid remained stable after processing.
• Comparison of PCR test results using RNA isolated from the processed samples to RNA extracted directly from the sample dilutions demonstrated that the integrity of the viral RNA was minimally affected by the processing step for the rapid test.
• Table 4 Lanes of Agarose Gel of FIG. 3.
• FIG. 3 demonstrates both formulation A and formulation B are compatible with use of the processed sample for RNA extraction and PCR testing.
• Storage of the processed samples at 4°C for up to 24 hours prior to RNA extraction suggests little degradation of the viral RNA occurred in samples processed with either formulation.
• prolonged storage of the extracted samples at RT demonstrated decreased PCR performance, possibly due to viral RNA degradation over time (lanes 8, 10) .
• stabilization transport diluents Two potential stabilization transport diluents were examined in an attempt to increase stability of viral RNA in samples processed for POC testing.
• the stabilization transport diluent was designed to help maintain the integrity of nucleic acids present in the sample.
• Various formulations are possible where optimal pH conditions, buffer types, salts, chelating agents, enzyme inhibitors, nucleic acid binding proteins, chaotropes, etc. may be employed.
• Stabilization transport diluent A contained Qiagen viral RNA lysis/binding buffer.
• Stabilization transport diluent B contained 6 M guanidine thiocyanate + 20 mM EDTA. Aliquots of an H1N1 positive clinical specimen were processed using rapid test processing reagent B.
• the processed samples were immediately used for RNA extraction or mixed with one of the two different stabilization transport diluents and stored at 4°C for up to six days prior to RNA extraction. A portion of the extracted RNA samples was then used as target for RT-PCR with primers specific for the matrix gene of the influenza A virus.
• the RT-PCR results are shown in FIG. 4.
• Table 5 shows the processing conditions corresponding to each lane of the agarose gel of the RT-PCR results shown in FIG. 4.
• Table 5 Lanes of Agarose Gel of FIG. 4.
• a stabilization transport diluent was used in an attempt to increase stability of the viral RNA in samples processed for POC testing, particularly when samples are stored for extended periods of time at room temperature.
• Aliquots of an HlNl positive clinical specimen were processed using rapid test processing reagent formulation B described in Example 3, and the processed samples were immediately used for RNA extraction, or mixed with stabilization transport diluent A and stored at RT and 4°C for up to seven days prior to RNA extraction.
• a portion of the extracted RNA samples was then used as target for RT-PCR with primers specific for the matrix gene of the influenza A virus.
• the PCR results are shown in FIG. 5.
• Table 6 shows the processing conditions corresponding to each lane of the agarose gel of the RT-PCR results shown in FIG. 5.
• Table 6 Lanes of Agarose Gel of FIG. 5.
• FIG. 5 demonstrates that intact viral RNA can be extracted from processed samples mixed with the stabilization transport diluent after storage of the samples for up to 7 days at 4°C or up to 4 days at room temperature.
• Stabilization transport diluent B was used to examine stabilization properties across different influenza strains: A: Influenza A strain A/Solomon Island/03/06 (H1N1) ; B: Influenza A strain A/Wisconsin/67/2005 (H3N2); and C: Influenza B strain B/Jiangsu/10/2003.
• Table 7 Table 6: Lanes of Agarose Gel of FIG. 6.
• FIG. 6 demonstrates that intact viral RNA from various strains can be extracted from processed samples mixed with the stabilization transport diluent after storage of the samples for up to 7 days at 4°C or up to 14 days at -20°C.
• intact viral RNA was extracted after storage under all conditions .
• FIG. IB Utility of one embodiment of the method of the present invention illustrated in FIG. IB was demonstrated in a clinical trial performed during the 2010-2011 influenza season. Paired nasopharyngeal (NPS) or upper nasal swabs
• NS were collected from patients enrolled in the POC influenza study.
• One swab was processed directly for use in an investigational rapid immunoassay at the POC site and then a portion (3 to 5 drops) of the remaining sample was mixed with the stabilization transport diluent B (200 ⁇ ) and stored at either 2 to 8°C for up to 5 days or -20°C for up to two weeks prior to being sent to a laboratory for PCR analysis.
• the second swab was placed in 3 ml of viral transport media and sent directly to a clinical laboratory for PCR testing.
• R A was extracted using the Qiagen Viral RNA miniprep kit according to the manufacturer.
• RNA samples Five microliters of extracted RNA was used for PCR amplification using a Cepheid SmartCycler II instrument according to the assay procedure described in the Prodesse ProFlu+ package insert . Interpretation of PCR results for specimens and controls was determined using the Cepheid SmartCycler Dx software according to the protocols outlined in the Prodesse ProFlu+ package insert. The positive and negative percent agreement between results obtained from the POC stabilized sample (POC PCR) and the swab- in-transport media sample (Reference PCR) are shown below in Table 7.
• Table 7 demonstrates that samples can be processed for rapid POC testing and a portion of that processed sample can be used for lab-based testing such as PCR. Greater than 91.9% agreement was obtained in various viral strains when comparing a sample that was directly processed for PCR to a sample that was first processed under conditions optimal for rapid POC testing and then subsequently processed for PCR.

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