Systems and methods for detecting infectious diseases

Patent metadata

Field	Value
Publication number	US-9916428-B2
Application number	US-201514604194-A
Country	US
Kind code	B2
Filing date	Jan 23, 2015
Priority date	Sep 6, 2013
Publication date	Mar 13, 2018
Grant date	Mar 13, 2018

Abstract

Systems, methods, and devices for detecting infections in a clinical sample are provided. Small-volume clinical samples obtained at a point-of-service (POS) location and may be tested at the POS location for multiple markers for multiple diseases, including upper and lower respiratory diseases. Samples may be tested for cytokines, or for inflammation indicators. Dilution of samples, or levels of detection, may be determined by the condition or past history of a subject. Test results may be obtained within a short amount of time after sample placement in a testing device, or within a short amount of time after being obtained from the subject. A prescription for treatment of a detected disorder may be provided, and may be filled, at the POS location. A bill may be automatically generated for the testing, or for the prescription, may be automatically sent to an insurance provider, and payment may be automatically obtained.

First claim

What is claimed is:

1. A method of detecting at least one nucleic acid disease marker in a clinical sample, comprising:
a) introducing at least a portion of said clinical sample into an automatic sample processing device configured for performing immunoassays and nucleic acid amplification assays, wherein said automatic sample processing device comprises:
i) a sample handling system configured to transport said at least a portion of the clinical sample; and
ii) a detector;

b) performing an isothermal nucleic acid amplification reaction without thermal cycling for the detection of a nucleic acid disease marker present on a target nucleic acid in the at least a portion of the clinical sample, or an aliquot thereof, wherein said target nucleic acid comprises a double-stranded nucleic acid having a first strand and a second strand and said nucleic acid disease marker comprises a template region of the target nucleic acid, wherein said performing comprises contacting the at least a portion of the clinical sample, or an aliquot thereof, with a nucleic acid amplification reagent and isothermally amplifying said nucleic acid disease marker at a high temperature without thermal cycling, wherein said nucleic acid amplification reagent comprises:
a nucleic acid polymerase having strand-displacement activity, and
a first primer and a second primer, said primers having template-binding regions and having tail regions, wherein said primer template-binding regions are complementary to at least a portion of said template region of the nucleic acid disease marker, said tail regions containing 5′ terminal nucleotides of the primers, and wherein said tail region of said first primer is complementary to said tail region of said second primer, and wherein said isothermal nucleic acid amplification reaction comprises:
1) generating an extension product of the first primer by treating the target nucleic acid with said polymerase having strand displacement activity and treating the first primer under conditions such that the template-binding region of the first primer anneals to said first strand of the target nucleic acid;
2) generating an extension product of the second primer by treating the extension product of the first primer with said polymerase having strand displacement activity and treating the second primer under conditions such that the template-binding region of the second primer anneals to the extension product of the first primer;
3) repeating steps 1) and 2) to provide further extension products comprising partially double-stranded nucleic acids comprising at least one tail-region sequence of the first primer tail and comprising at least one tail-region sequence of the second primer tail, wherein said extension product comprises a double-stranded portion in which at least a portion of said first primer tail-region sequence is hybridized to at least a portion of said second primer tail-region sequence;
4) generating a concatamer strand, wherein said concatamer strand is generated as a result of the annealing of at least two hybridized tail sequences from at least two partially double-stranded nucleic acid strands to generate cross-over structures;
c) obtaining data measurements with the aid of said detector; and
d) detecting at least one nucleic acid disease marker.

2. The method of claim 1 , comprising detecting two or more nucleic acid disease markers in two or more aliquots thereof, wherein said detecting comprises isothermal amplification of two or more nucleic acid disease markers at high temperature without thermal cycling.

3. The method of claim 1 , further comprising performing an immunoassay for the detection of a further disease marker in the at least a portion of a sample, or in one or more aliquots thereof, wherein said further disease marker is other than a nucleic acid disease marker.

4. The method of claim 1 , wherein said measurements are obtained over a period of time, and wherein these measurements are indicative of the progress of the nucleic acid amplification reaction over said period of time.

5. The method of claim 1 , wherein said nucleic acid amplification is performed within a moveable assay unit.

6. The method of claim 3 , wherein said immunoassay is performed within a moveable assay unit.

7. The method of claim 3 , wherein both said nucleic acid assay and said immunoassay are performed within a moveable assay unit.

8. The method of claim 1 , wherein said sample handling system is configured to transport a moveable assay unit.

9. The method of claim 1 , wherein said clinical sample is a small-volume clinical sample having a volume of less than about 500 microliters.

10. The method of claim 1 , wherein the method is a point-of service (POS) method performed at a POS location.

11. The method of claim 10 , comprising point-of-service (POS) methods performed at a POS location, wherein the period of time from initiating said method of detecting to detecting said at least one nucleic acid disease marker is less than about 40 minutes.

12. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises a nucleic acid marker selected from the group consisting of an inflammatory marker for infectious disease, an influenza marker, a marker for an upper respiratory disease, a marker for a lower respiratory disease, and a marker for a sexually transmitted disease.

13. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises a nucleic acid marker for a respiratory disease selected from the group consisting of adenovirus B, adenovirus C, adenovirus E, Bordetella pertussis, mycobacterium tuberculosis (MTB), Staphylococcus aureus , Methicillin-Resistant Staphylococcus aureus (MRSA), Group A streptococcus , Group B streptococcus, Moraxella catarrhalis, Enterobacter aerogenes, Haemophilus parainfluenzae , Metapneumo Virus, Streptococcus pneumonia , Parainfluenza Virus 1, Parainfluenza Virus 2, Parainfluenza Virus 3, Coronavirus OC43, Coronavirus NL63, Coronavirus MERS, Coronavirus HKU1, Coronavirus 229E, Klibsiella pneumonia phoE, Klebsiella pneumonia KPC, Bocavirus type 2,4, and Bocavirus type 1,3.

14. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises a nucleic acid marker for a disease caused by a disease-causing agent selected from adenovirus B, adenovirus C, adenovirus E, Bordetella pertussis, mycobacterium tuberculosis (MTB), Staphylococcus aureus , Methicillin-Resistant Staphylococcus aureus (MRSA), Group A streptococcus , and Group B streptococcus.

15. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises an influenza marker.

16. The method of claim 15 , wherein the nucleic acid disease marker comprises an influenza marker selected from a marker for H1N1 (seasonal) influenza, H1N1 (novel) influenza, a marker for H3N2 influenza, a marker for H7N9 influenza, a marker for H5N1 influenza, and a nucleic acid sequence encoding an influenza matrix protein or portion thereof.

17. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises a marker for a sexually transmitted disease.

18. The method of claim 1 , wherein said at least one nucleic acid disease marker comprises a marker for a sexually transmitted disease, wherein the disease is caused by an agent selected from the group consisting of human immunodeficiency virus (HIV), HIV-2 Group A, HIV-2, Group B, HIV-1 Group M, Hepatitis B, Hepatitis Delta, herpes simplex virus (HSV), streptococcus B, and treponema pallidum.

Assignees

• Theranos Inc
• Theranos Ip Co Llc

Inventors

• Patel Pranav
• Tabakman Scott
• Belhocine Kamila
• Richardson Aaron
• Lee Josephine
• Lui Clarissa

Classifications

• G16H50/20

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• G01N33/56933

  Mycoplasma · CPC title

• C12Q1/703

  Viruses associated with AIDS · CPC title

• C12Q1/701

  Specific hybridization probes · CPC title

• C12Q1/689

  for bacteria · CPC title