Nmr systems and methods for the rapid detection of analytes

Abstract

This invention features systems and methods for the detection of analytes, and their use in the treatment and diagnosis of disease.

What is claimed is: 
     
         1 . A method for detecting the presence of a virus in a sample, the method comprising:
 (a) providing a sample from a subject suspected of having a virus;   (b) disrupting the virus in the sample to produce a mixture comprising viral nucleic acids;   (c) placing the mixture (b) in a container and amplifying a target nucleic acid in the mixture to form an amplified mixture solution comprising the target nucleic acid, wherein the target nucleic acid is characteristic of the virus to be detected;   (d) following step (c), mixing the amplified mixture solution with from 1×10 6  to 1×10 13  magnetic particles per milliliter of the amplified mixture solution to form a liquid sample, wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm, a T 2  relaxivity per particle of from 1×10 8  to 1×10 12  mM −1 s −1 , and binding moieties on their surface, the binding moieties operative to alter aggregation of the magnetic particles in the presence of the target nucleic acid or a multivalent binding agent;   (e) placing the liquid sample in a device, the device comprising a support defining a well for holding the detection tube comprising the magnetic particles and the target nucleic acid, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using one or more magnets and an RF pulse sequence;   (f) exposing the liquid sample to a bias magnetic field and an RF pulse sequence;   (g) following step (f), measuring the signal from the liquid sample; and   (h) on the basis of the result of step (g), detecting the virus,   
       wherein the method is capable of detecting fewer than 100 virus copies in the sample. 
     
     
         2 . The method of  claim 1 , wherein the virus is selected from the group consisting of a polyomavirus, cytomegalovirus (CMV), Epstein Barr virus (EBV), BK virus, hepatitis B virus (HBV), hepatitis C virus (HCV), herpes simplex virus 1 (HSV1), herpes simplex virus 2 (HSV2), respiratory syncytial virus (RSV), Influenza A, Influenza A subtype H1, Influenza A subtype H3, Influenza B, human herpesvirus 6 (HHV-6), human herpesvirus 8 (HHV-8), human metapneumovirus (hMPV), rhinovirus, Parainfluenza 1, Parainfluenza 2, Parainfluenza 3, and adenovirus. 
     
     
         3 . The method of  claim 2 , wherein the polyomavirus is a John Cunningham virus (JC virus). 
     
     
         4 . The method of  claim 3 , wherein the subject has progressive multifocal leukoencephalopathy. 
     
     
         5 . The method of  claim 1 , wherein the mixture (b) is produced by mixing from 0.05 to 4.0 mL of the sample with a lysis agent. 
     
     
         6 . The method of  claim 1 , wherein the sample is a biological sample. 
     
     
         7 . The method of  claim 6 , wherein the biological sample is selected from the group consisting of whole blood, cerebrospinal fluid (CSF), sweat, tears, urine, saliva, semen, serum, plasma, feces, vaginal fluid or tissue, sputum, nasopharyngeal aspirate or swab, lacrimal fluid, mucous, tissues, organs, bones, teeth, and tumors. 
     
     
         8 . The method of  claim 7 , wherein the biological sample is whole blood. 
     
     
         9 . The method of  claim 8 , wherein the method further comprises lysing red blood cells of the whole blood sample prior to step (b). 
     
     
         10 . The method of  claim 9 , further comprising concentrating the viral particles resulting from the lysis of red blood cells. 
     
     
         11 . The method of  claim 10 , wherein the magnetic particles are used to concentrate the viral particles. 
     
     
         12 . The method of  claim 7 , wherein the biological sample is CSF. 
     
     
         13 . The method of  claim 1 , wherein the magnetic particles have a mean diameter between 700 and 900 nm. 
     
     
         14 . The method of  claim 13 , wherein the magnetic particles have a mean diameter between 700 and 850 nm. 
     
     
         15 . The method of  claim 1 , wherein steps (a) through (g) are completed within 3 hours. 
     
     
         16 . The method of  claim 1  or  15 , wherein the magnetic particles comprise one or more populations having a first probe and a second probe conjugated to their surface, the first probe operative to bind to a first segment of the target nucleic acid and the second probe operative to bind to a second segment of the target nucleic acid, wherein the magnetic particles form aggregates in the presence of the target nucleic acid. 
     
     
         17 . The method of  claim 1  or  15 , wherein the magnetic particles comprise a first population having a first binding moiety on their surface and a second population having a second binding moiety on their surface, and the multivalent binding moiety comprising a first probe and a second probe, the first probe operative to bind to said first binding moiety and the second probe operative to bind to a second binding moiety, the binding moieties and multivalent binding moiety operative to alter an aggregation of the magnetic particles in the presence of the target nucleic acid. 
     
     
         18 . A method for detecting the presence of a virus in a viral filtrate, the method comprising:
 (a) providing a viral filtrate obtained from a sample from a subject suspected of having a virus;   (b) disrupting the virus in the viral filtrate to produce a mixture comprising viral nucleic acids;   (c) placing the mixture (b) in a container and amplifying a target nucleic acid in the mixture to form an amplified mixture solution comprising the target nucleic acid, wherein the target nucleic acid is characteristic of the virus to be detected;   (d) following step (c), mixing the amplified mixture solution with from 1×10 6  to 1×10 13  magnetic particles per milliliter of the amplified mixture solution to form a liquid sample, wherein the magnetic particles have a mean diameter of from 150 nm to 1200 nm, a T 2  relaxivity per particle of from 1×10 8  to 1×10 12  mM −1 s −1 , and binding moieties on their surface, the binding moieties operative to alter aggregation of the magnetic particles in the presence of the target nucleic acid or a multivalent binding agent;   (e) placing the liquid sample in a device, the device comprising a support defining a well for holding the detection tube comprising the magnetic particles and the target nucleic acid, and having an RF coil disposed about the well, the RF coil configured to detect a signal produced by exposing the liquid sample to a bias magnetic field created using one or more magnets and an RF pulse sequence;   (f) exposing the liquid sample to a bias magnetic field and an RF pulse sequence;   (g) following step (f), measuring the signal from the liquid sample; and   (h) on the basis of the result of step (g), detecting the virus,   wherein the method is capable of detecting fewer than 100 virus copies in the sample.