Abstract:
A method for using a single sample suspected of containing a microorganism for both a local rapid test immunoassay and a remote laboratory test. The sample is collected from a patient at a physician&#39;s office or from the environment to be tested. The sample is collected using a swab or other implement, combined with a rapid test processing reagent and a portion of the processed sample is used for the local rapid test. The rapid test processing reagent typically consists of a buffer, a salt, and a detergent and is compatible with the local rapid test immunoassay. Only a portion of the processed sample is used for the local rapid test, leaving a remaining portion of the processed sample to be used in a remote laboratory assay. At least some of the remaining portion of the processed sample is combined with a stabilization agent that preserves at least the nucleic acid in the processed sample for the remote laboratory assay.

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    This application claims the benefit of the filing date of U.S. Provisional Patent Application No. 61/366,076, filed Jul. 20, 2010, the disclosure of which is hereby incorporated herein by reference. 
     
    
     BACKGROUND OF THE INVENTION 
       [0002]    The linkage between point of care (POC) rapid testing and laboratory-based testing has typically been addressed through preservation of samples to support culture-based laboratory testing methods. Currently, samples collected at the POC site are either processed and used directly in a rapid test (the portion of the processed sample not used in the rapid test being discarded); or diluted in liquid transport media to enable transfer for laboratory-based testing such as rapid immunoassay, culture and/or polymerase chain reaction (PCR). Specimens that generate negative results from a POC test are often reflex tested—the negative result is confirmed by lab-based testing methods such as PCR. In addition, specimens that generate positive POC test results are frequently tested for additional characterizations such as subtyping or other epidemiologic information. 
         [0003]    Referring to  FIG. 1 , at physician office POC sites (and other non-laboratory sites where patients are seen or samples for rapid testing are collected), 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&#39;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. With the current methods, a physician (or other administrator of a POC rapid test) cannot perform both a POC rapid test and a lab-based test using the sample collected at the site (e.g. the physician&#39;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 . However, 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. 
         [0004]    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. In addition, although collected from the same patient, 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. 
       SUMMARY OF THE INVENTION 
       [0005]    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 (confirmatory testing or other laboratory tests such as diagnostic and identification testing) through the use of a single sample collected and subjected to a rapid test at the POC. 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. Typically, 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. According to one embodiment of the present invention, 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. In other embodiments the remainder is not further diluted, but is still subjected to a laboratory-test. For purposes of the present invention, 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. In the context of the invention, 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. 
         [0006]    The methods described herein can be applied to rapid immunoassays used at POC for rapid diagnosis leading to a critical treatment decision. Rapid immunoassays for use at a POC site are well known and commercially available. They are not described in detail herein. For example, 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. 
         [0007]    In another embodiment, 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. 
         [0008]    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. In one embodiment, the molecular diagnostic test is nucleic acid-based. In a preferred embodiment, the nucleic acid-based diagnostic test is PCR. 
         [0009]    In another embodiment of the invention, different 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. One skilled in the art is aware of the suitable constituents and conditions (e.g. pH) for a stabilization transport diluent for a particular application. For example, if 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. In certain embodiments of the present invention, the remainder of the processed sample not used for the rapid test may be added to the stabilization transport diluent. In one embodiment, the stabilization transport diluent may already be present in the rapid test processing reagent used for the POC test. In another embodiment, 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. In a preferred embodiment, the stabilization transfer diluent stabilizes nucleic acids in the sample. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0010]      FIG. 1A  illustrates the prior art method for the standard protocol for POC and lab-based testing. 
           [0011]      FIG. 1B  illustrates the method for POC and lab-based testing of the present invention. 
           [0012]    FIG.  2 A/B demonstrates the results from RT-PCR for Influenza A from samples processed for POC testing under various dilution conditions. 
           [0013]      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. 
           [0014]      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. 
           [0015]      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. 
           [0016]      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. 
       
    
    
     DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS 
       [0017]      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. In the alternative standard protocol, 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 . In this situation, 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. 
         [0018]      FIG. 1B  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 . In the alternative, 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. In this regard, 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. 
         [0019]    There are a variety of rapid tests that are currently commercially available. Such rapid tests are not described in detail herein, but are available from a variety of sources including Becton Dickinson, Alere, Quidel, Meridian, Genzyme, etc. The invention is not limited to use with a particular rapid test. 
       EXAMPLES 
       [0020]    The following examples illustrate various embodiments of the invention and are not meant to limit the invention except in a manner consistent with the claims presented herein. 
       Example 1 
       [0021]    The ability to detect influenza viral RNA in samples processed for use in a POC rapid immunoassay was demonstrated using an H1N1 positive clinical specimen collected by upper nasal swab from an individual exhibiting positive flu symptoms. The swab was placed in 3 ml of commercially available transport media (BD™ Universal Viral Transport Media available from Becton Dickinson) and confirmation that the sample tested positive for H1N1 was obtained. For testing, certain 50 μl aliquots of that specimen were obtained. One aliquot was mixed directly with a rapid test processing reagent for the immunoassay and others were further diluted (5×, 25×, 125× or 625×) with stabilization transport diluent prior to mixing with the rapid test processing reagent. Each 50 μl aliquot of sample was combined with 25 μl of rapid test processing reagent. The rapid test processing reagent (tris buffer, NaCl, 6% detergent and pH adjusted to 8.0) was optimized to release and preserve the influenza nucleoprotein which is the target antigen for the rapid immunoassay. The immunoassay testing results on the various sample dilutions are shown in Table 1. 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Immunoassay Results 
               
             
          
           
               
                   
                 H1N1 Clinical Sample 
                 Rapid Immunoassay Result 
               
               
                   
                   
               
               
                   
                 undiluted 
                 Flu A positive/Flu B negative 
               
               
                   
                 1:5 dilution 
                 Flu A positive/Flu B negative 
               
               
                   
                 1:25 dilution 
                 Flu A negative/Flu B negative 
               
               
                   
                 1:125 dilution 
                 Flu A negative/Flu B negative 
               
               
                   
                 1:625 dilution 
                 Flu A negative/Flu B negative 
               
               
                   
                   
               
             
          
         
       
     
         [0022]    The immunoassay test results in Table 1 demonstrate the effect of specimen dilution on rapid test performance. Samples diluted greater than 1:5 resulted in a negative rapid immunoassay test. In order to provide optimal POC clinical performance, 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. However, standard POC testing methods using direct swab samples, as noted above, do not enable lab-based testing because of initial placement of such samples into a transport diluent. 
       Example 2 
       [0023]    Aliquots (50 μl) of each dilution prepared in Example 1 were mixed with 25 μl rapid test processing reagent. One set of processed samples was stored at room temperature (RT) for 5 minutes prior to RNA extraction using a Qiagen Viral RNA miniprep kit according to the manufacturer&#39;s instructions. Additional sets of processed samples were stored for 4 hours at either 4° C. or RT prior to RNA extraction. A 5 μl portion of the extracted RNA samples was then used as target for reverse transcription-polymerase chain reaction (RT-PCR) with primers specific for the matrix gene of influenza A virus. The RT-PCR results are shown in  FIGS. 2A and 2B . Tables 2 and 3 show the processing conditions corresponding to each lane of the agarose gel of the RT-PCR results shown in  FIGS. 2A and 2B . 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Lanes of Agarose Gel of FIG. 2A 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Molecular Weight Marker 
                 M 
               
               
                   
                 Sample diluted 1:5, processed 
                 1 
               
               
                   
                 for rapid test, RNA 
               
               
                   
                 extraction immediately 
               
               
                   
                 Sample diluted 1:5, processed 
                 2 
               
               
                   
                 for rapid test, stored at 4° C. 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample diluted 1:5, processed 
                 3 
               
               
                   
                 for rapid test, stored at 
               
               
                   
                 Room Temperature for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample diluted 1:25, 
                 4 
               
               
                   
                 processed for rapid test, RNA 
               
               
                   
                 extraction immediately 
               
               
                   
                 Sample diluted 1:25, 
                 5 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at 4° C. for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample diluted 1:25, 
                 6 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at Room Temperature 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample diluted 1:5, RNA 
                 7 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:25, RNA 
                 8 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:125, RNA 
                 9 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:625, RNA 
                 10 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Lanes of Agarose Gel of FIG. 2B 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Molecular Weight Marker 
                 M 
               
               
                   
                 Sample diluted 1:125, 
                 11 
               
               
                   
                 processed for rapid test, RNA 
               
               
                   
                 extraction immediately 
               
               
                   
                 Sample diluted 1:125, 
                 12 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at 4° C. for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample diluted 1:125, 
                 13 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at Room Temperature 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample diluted 1:625, 
                 14 
               
               
                   
                 processed for rapid test, RNA 
               
               
                   
                 extraction immediately 
               
               
                   
                 Sample diluted 1:625, 
                 15 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at 4° C. for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample diluted 1:625, 
                 16 
               
               
                   
                 processed for rapid test, 
               
               
                   
                 stored at Room Temperature 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample diluted 1:5, RNA 
                 17 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:25, RNA 
                 18 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:125, RNA 
                 19 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                 Sample diluted 1:625, RNA 
                 20 
               
               
                   
                 extraction (no rapid test/no 
               
               
                   
                 rapid test reagent) 
               
               
                   
                   
               
             
          
         
       
     
         [0024]      FIGS. 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 (lanes 7-10, 17-20) demonstrated that the integrity of the viral RNA was minimally affected by the processing step for the rapid test. 
       Example 3 
       [0025]    The stability of viral RNA in processed samples was examined using two different rapid test processing reagents optimized for use in the rapid immunoassay for influenza A/B. Sample processing for rapid immunoassays typically involves the use of a relatively gentle lysis treatment mediated by a reagent containing various salts and detergents. Two different formulations for the rapid test processing reagent were examined for compatibility with the described method. Formulation A contained Tris buffer, NaCl, 16% detergent at a pH of 7.8. Formulation B contained Tris buffer, NaCl, 6% detergent at a pH of 8.0. Aliquots of an H1N1 positive clinical specimen described in Example 1 were processed with both formulations, and the processed samples were used immediately for RNA extraction using the Qiagen Viral RNA miniprep kit, or stored at RT and 4° C. for up to 24 hours 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. 3 . Table 4 shows the processing conditions corresponding to each lane of the agarose gel of the RT-PCR results shown in  FIG. 3 . 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 Lanes of Agarose Gel of FIG. 3. 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Molecular Weight Marker 
                 M 
               
               
                   
                 Sample processed with rapid 
                 1 
               
               
                   
                 test processing reagent A, 
               
               
                   
                 RNA extraction immediately 
               
               
                   
                 Sample processed with rapid 
                 2 
               
               
                   
                 test processing reagent A, 
               
               
                   
                 stored at 4° C. for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample processed with rapid 
                 3 
               
               
                   
                 test processing reagent A, 
               
               
                   
                 stored at 4° C. for 24 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample processed with rapid 
                 4 
               
               
                   
                 test processing reagent B, 
               
               
                   
                 RNA extraction immediately 
               
               
                   
                 Sample processed with rapid 
                 5 
               
               
                   
                 test processing reagent B, 
               
               
                   
                 stored at 4° C. for 4 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample processed with rapid 
                 6 
               
               
                   
                 test processing reagent B, 
               
               
                   
                 stored at 4° C. for 24 hrs 
               
               
                   
                 before RNA extraction 
               
               
                   
                 Sample processed with rapid 
                 7 
               
               
                   
                 test processing reagent A, 
               
               
                   
                 stored at room temperature 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample processed with rapid 
                 8 
               
               
                   
                 test processing reagent A, 
               
               
                   
                 stored at room temperature 
               
               
                   
                 for 24 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample processed with rapid 
                 9 
               
               
                   
                 test processing reagent B, 
               
               
                   
                 stored at room temperature 
               
               
                   
                 for 4 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                 Sample processed with rapid 
                 10 
               
               
                   
                 test processing reagent B, 
               
               
                   
                 stored at room temperature 
               
               
                   
                 for 24 hrs before RNA 
               
               
                   
                 extraction 
               
               
                   
                   
               
             
          
         
       
     
         [0026]      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. However, prolonged storage of the extracted samples at RT demonstrated decreased PCR performance, possibly due to viral RNA degradation over time (lanes 8, 10). 
       Example 4 
       [0027]    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 . 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 Lanes of Agarose Gel of FIG. 4. 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Molecular Weight Marker 
                 M 
               
               
                   
                 Sample processed for rapid 
                 1 
               
               
                   
                 test, RNA extraction 
               
               
                   
                 immediately 
               
               
                   
                 Sample processed for rapid 
                 2 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent A, stored at 4° C. for 
               
               
                   
                 3 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 3 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent B, stored at 4° C. for 
               
               
                   
                 3 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 4 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent A, stored at 4° C. for 
               
               
                   
                 6 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 5 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent B, stored at 4° C. for 
               
               
                   
                 6 days before RNA extraction 
               
               
                   
                   
               
             
          
         
       
     
         [0028]    Using either formulation of the stabilization transport diluent, intact viral RNA was extracted from samples processed for POC testing that had been stored for up to 6 days at 4° C. Comparing the PCR results from the stored samples (lanes 2-5) to those obtained using RNA extracted immediately after processing (lane 1) suggest little, if any, degradation of the viral RNA occurred over time in the processed samples treated with either stabilization transport diluent. 
       Example 5 
       [0029]    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 H1N1 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 . 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 Lanes of Agarose Gel of FIG. 5. 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Molecular Weight Marker 
                 M 
               
               
                   
                 Sample processed for rapid 
                 1 
               
               
                   
                 test, RNA extraction 
               
               
                   
                 immediately 
               
               
                   
                 Sample processed for rapid 
                 2 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at 4° C. for 3 
               
               
                   
                 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 3 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at 4° C. for 4 
               
               
                   
                 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 4 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at 4° C. for 5 
               
               
                   
                 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 5 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at 4° C. for 6 
               
               
                   
                 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 6 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at 4° C. for 7 
               
               
                   
                 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 7 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at room 
               
               
                   
                 temperature for 1 day before 
               
               
                   
                 RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 8 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at room 
               
               
                   
                 temperature for 2 days before 
               
               
                   
                 RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 9 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at room 
               
               
                   
                 temperature for 3 days before 
               
               
                   
                 RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 10 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluent, stored at room 
               
               
                   
                 temperature for 4 days before 
               
               
                   
                 RNA extraction 
               
               
                   
                   
               
             
          
         
       
     
         [0030]    Mixing the processed sample with a stabilization transport diluent increased the stability of the viral nucleic acid, and enabled longer-term storage and transport of the processed sample at various temperatures.  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. 
       Example 6 
       [0031]    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. Aliquots (50 μl) of cell culture supernatants from cultures into which virus had been introduced from nasal swabs of a patient exhibiting symptoms of influenza and these aliquots were combined with rapid test processing reagent B (25 μl) and the processed samples were either immediately used for RNA extraction, or mixed with stabilization transport diluent B (75 μl) and stored at 4° C. or −20° C. for up to fourteen days prior to RNA extraction. A portion of the extracted RNA samples was then used as target for RT-PCR reactions with primers specific for the matrix gene of influenza A or the nucleoprotein gene of influenza B. The PCR results are shown in  FIG. 6 . Table 7 shows the processing conditions corresponding to each lane of the agarose gel of the RT-PCR results shown in  FIG. 6 . 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Table 6: Lanes of Agarose Gel of FIG. 6. 
               
             
          
           
               
                   
                   
                 Lane on 
               
               
                   
                 Processing Method 
                 Agarose Gel 
               
               
                   
                   
               
               
                   
                 Sample processed for rapid 
                 1 
               
               
                   
                 test, RNA extraction 
               
               
                   
                 immediately 
               
               
                   
                 Sample processed for rapid 
                 2 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluents B, stored at 4° C. for 
               
               
                   
                 2 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 3 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluents B, stored at 4° C. for 
               
               
                   
                 7 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 4 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluents B, stored at 4° C. for 
               
               
                   
                 10 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 5 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluents B, stored at 4° C. for 
               
               
                   
                 14 days before RNA extraction 
               
               
                   
                 Sample processed for rapid 
                 6 
               
               
                   
                 test, mixed with 
               
               
                   
                 stabilization transport 
               
               
                   
                 diluents B, stored at −20° C. 
               
               
                   
                 for 7 days before RNA 
               
               
                   
                 extraction 
               
               
                   
                   
               
             
          
         
       
     
         [0032]    Mixing the processed sample with a stabilization transport diluent increased the stability of the viral nucleic acid in all three strains of Influenza for up to 14 days at 4° C. or up to 7 days at −20° C.  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. For both the A and B strains, intact viral RNA was extracted after storage under all conditions. 
       Example 7 
       [0033]    Utility of one embodiment of the method of the present invention illustrated in  FIG. 1B  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 μl) 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. 
         [0034]    All PCR testing was performed using the Prodesse ProFlu+ assay available from GenProbe, Inc. (San Diego, Calif.). The Prodesse ProFlu+ test is FDA-cleared and is able to detect and differentiate Influenza A, Influenza B, and RSV in respiratory specimens. For the swab-in-transport media specimens, RNA was extracted using the NucliSENS easyMAG System (bioMérieux) according to the Prodesse ProFlu+ package insert. For the POC processed samples in the stabilization transport diluent, RNA was extracted using the Qiagen Viral RNA miniprep kit according to the manufacturer. 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. 
         [0000]    
       
         
               
             
               
               
               
             
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
               
               
               
               
               
             
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Comparison of PCR results from POC processed samples 
               
               
                 compared to Reference PCR 
               
             
          
           
               
                 Influenza A 
                 Influenza B 
                 RSV 
               
             
          
           
               
                   
                 Reference 
                   
                 Reference 
                   
                 Reference 
                   
               
               
                   
                 PCR 
                   
                 PCR 
                   
                 PCR 
               
             
          
           
               
                 POC PCR 
                 P 
                 N 
                   
                 POC PCR 
                 P 
                 N 
                   
                 POC PCR 
                 P 
                 N 
               
               
                   
               
             
          
           
               
                 P 
                 150 
                 22 
                 172 
                 P 
                 91 
                 12 
                 103 
                 P 
                 18 
                 2 
                 20 
               
               
                 N 
                 5 
                 335 
                 340 
                 N 
                 8 
                 401 
                 409 
                 N 
                 1 
                 491 
                 492 
               
               
                   
                 155 
                 357 
                 512 
                   
                 99 
                 413 
                 512 
                   
                 19 
                 493 
                 512 
               
             
          
           
               
                 Reference Method: 
                 Reference Method: 
                 Reference Method: 
               
               
                 PCR from swab in transport media 
                 PCR from swab in transport media 
                 PCR from swab in transport media 
               
               
                 Positive Percent Agreement: 96.8% 
                 Positive Percent Agreement: 91.9% 
                 Positive Percent Agreement: 94.7% 
               
               
                 Negative Percent Agreement: 93.8% 
                 Negative Percent Agreement: 97.1% 
                 Negative Percent Agreement: 99.6% 
               
               
                   
               
             
          
         
       
     
         [0035]    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. 
         [0036]    Although the invention herein has been described with reference to particular embodiments, it is to be understood that these embodiments are merely illustrative of the principles and applications of the present invention. It is therefore to be understood that numerous modifications may be made to the illustrative embodiments and that other arrangements may be devised without departing from the spirit and scope of the present invention as defined by the appended claims.