In vitro diagnostic system

Description

1 / 97 In Vitro Diagnostic System - Cross-reference to Related Requests

[001] This application claims priority to U.S. Provisional Patent Application 63 / 456,444 filed March 31, 2023 and 63 / 469,294 filed May 26, 2023, the disclosures of each of which are incorporated herein by reference in their entirety. BACKGROUND

[002] The ability to rapidly diagnose diseases—particularly highly infectious diseases—is fundamental to preserving human health. For example, the development and widespread use of rapid and accurate COVID-19 diagnostic tests allowed infected individuals to be quickly identified and isolated, which aided in containing the disease. The COVID-19 pandemic catalyzed the development and adoption of rapid tests for use in point-of-care (POC) or home settings worldwide, and the management of many other infectious diseases can be improved by enhanced diagnostic testing. SUMMARY

[003] Devices, systems, and diagnostic methodologies useful for detecting target nucleic acid sequences are provided in this document. The devices, as provided in this document, can be run in a point-of-care (POC) environment or home environment without specialized equipment. The devices according to this disclosure are low cost and easy to use.

[004] In one aspect, the present embodiments are directed to a method and a system for identifying an attribute of a cartridge being inserted into an electronic reader which includes: providing mar Petition 870250102472, dated 10 / 11 / 2025, page 7 / 197 2 / 97 identification mark(s) on a cartridge label (or on the cartridge itself) so that one or more LEDs inside the reader can illuminate the identification mark(s), allowing one or more photodetectors inside the reader to measure an optical signature of each identification mark. The cartridge attribute may be indicative of one or more tests that can be performed using the cartridge in conjunction with the reader.

[005] In one aspect, the present embodiments are directed to a method for identifying an attribute of a cartridge configured to be inserted into an electronic reader, the method including: providing the electronic reader, the electronic reader including at least one internal LED, at least one internal photodetector and at least one internal microprocessor communicatively coupled to at least one photodetector and at least one LED; providing the cartridge, the cartridge including at least one identification mark; inserting the cartridge into the reader; illuminating, by means of at least one LED, at least one identification mark, thereby creating an illuminated identification mark; detecting, by the photodetector, an optical signature of the illuminated identification mark; and identifying, by means of at least one microprocessor, at least one attribute of the cartridge based on the illuminated identification mark.

[006] In some models, the illumination of at least one identification mark occurs when the cartridge is inserted into the electronic reader.

[007] In some forms, at least one identifying mark includes at least one barcode.

[008] In some embodiments, at least one LED includes at least one first LED and one second LED, wherein at least one barcode includes: a first barcode used to quantify the speed at which the cartridge is inserted into the electronic reader. Petition 870250102472, dated 10 / 11 / 2025, page 8 / 197 3 / 97 co, the first barcode being illuminated by the first LED; and a second barcode used to identify at least one attribute of the cartridge, the second barcode being illuminated by the second LED, and wherein at least one microprocessor uses the quantized speed to calibrate the optical signature of the second barcode, thus allowing an adequate determination of the cartridge identification to be made.

[009] In some embodiments, at least one internal photodetector includes at least one photodiode and one phototransistor.

[0010] In some embodiments, the LED includes at least one red LED and one blue LED.

[0011] In some embodiments, at least one internal photodetector includes a dual-mode photodetector configured to measure the light emitted from at least one LED within a first spectrum and a second spectrum, and the second spectrum does not overlap with the first spectrum.

[0012] In some embodiments, the first spectrum includes wavelengths in a range from about 600 nm to about 660 nm, and the second spectrum includes wavelengths in a range from about 730 nm to about 900 nm.

[0013] In some embodiments, at least one identification mark includes one or more marks printed on a label placed on a surface of the cartridge.

[0014] In some embodiments, at least one LED includes from about 4 to about 12 identification LEDs, the one or more printed marks comprise from about 4 to about 12 printed marks, each printed mark being positioned to correspond to a position of one of the identification LEDs, so that the presence or absence of a printed mark in a position can be detected by the identification LED in the corresponding position. Petition 870250102472, dated 10 / 11 / 2025, p. 9 / 197 4 / 97 tooth.

[0015] In some forms, the number of identification LEDs is greater than the number of printed markings.

[0016] In some embodiments, a unique combination of positions marked on the label is associated with the cartridge attribute.

[0017] In some embodiments, the attribute includes a type of one or more tests that can be performed using the cartridge.

[0018] In some embodiments, the microprocessor executes one or more pre-loaded routines based on the attribute that is determined as a result of the cartridge attribute identification method.

[0019] In some embodiments, one or more printed marks include one or more position detection features.

[0020] In some embodiments, one or more position detection features include: a first position detection feature positioned on the label such that a center line of the first position detection feature is positioned so as to be slightly above a center line of a first reader component when the cartridge is correctly positioned within the reader; and a second position detection feature positioned on the label such that a center line of the second position detection feature is positioned so as to be slightly below a center line of a second reader component when the cartridge is correctly positioned within the reader;the method including determining, by the microprocessor, whether or not the cartridge is correctly positioned within the reader based on: 1) the position of the first position detection feature relative to the first reader component and 2) the position of the second position detection feature relative to the second reader component, wherein each of the first component; Petition 870250102472, dated 10 / 11 / 2025, page 10 / 197 5 / 97 The first component and the second component includes at least one internal photodetector and at least one LED.

[0021] In some embodiments, where the reader is configured to identify the cartridge attribute based on multiple modes of operation, the multiple modes of operation include: static identification including identification of the attribute, through at least one identification mark and the reader, after the cartridge is inserted into the reader; and dynamic identification including identification of the attribute, through at least one identification mark and the reader, while the cartridge is being inserted into the reader.

[0022] In some embodiments, one or more printed marks are printed in black ink on the label on top of a background that is at least one of white and gray.

[0023] In some embodiments, the cartridge includes at least one lyophilized sphere disposed therein, at least one lyophilized sphere including at least one of a lyophilized lysis sphere and a lyophilized polymerase chain reaction (PCR) sphere.

[0024] In another aspect, the present embodiments are directed to a method that includes: obtaining a biological sample from a subject; incubating the biological sample with at least one of a reagent and a buffer, thereby producing a biological solution; performing a lysis step on the biological solution; passively cooling the biological solution; amplifying one or more target nucleic acids in the biological solution by isothermal amplification; incubating the biological solution with a composition including: a CRISPR / Cas enzyme with collateral cleavage activity; a guide RNA that hybridizes specifically with a target nucleic acid; and a detectably labeled nucleic acid probe, in which hybridization of the guide RNA with the target nucleic acid induces or enhances the collateral cleavage activity of the CRISPR / Cas enzyme and the CRISPR / Cas enzyme cleaves the nucleic acid probe. Petition 870250102472, dated 10 / 11 / 2025, p. 11 / 197 6 / 97 detectably labeled nucleic acid probe, wherein cleavage of the detectably labeled nucleic acid probe results in an increase in detectable labeling; and determination of the target nucleic acid being present in the biological sample based on the detection of an increase in detectable labeling.

[0025] In some embodiments, the lysis step includes a thermal lysis step carried out at a temperature in a range of about 70 degrees C to about 95 degrees C, and in which the thermal lysis step is carried out in a first heating zone.

[0026] In some embodiments, passively cooling the biological solution includes flowing the biological solution through an internal passage of a cartridge, wherein the internal passage is oriented vertically and wherein the flow of the biological solution through the internal passage includes gravity flow.

[0027] In some embodiments, the isothermal amplification step involves amplifying the biological solution at a temperature in a range of about 50 degrees C to about 70 degrees C, and the isothermal amplification step is carried out in a second heating zone.

[0028] In some embodiments, the isothermal amplification step includes loop-mediated isothermal amplification (LAMP).

[0029] In some embodiments, the detectably labeled nucleic acid probe is marked with a fluorescent label.

[0030] In some embodiments, the fluorescent label includes a fluorescent group at the 5' end and a quencher group at the 3' end.

[0031] In some embodiments, the determination of the target nucleic acid present in the biological sample includes: optically illuminating the biological solution; and detecting at least one fluorescent signature using at least one photodiode and one phototransistor, at least Petition 870250102472, dated 10 / 11 / 2025, p. 12 / 197 7 / 97 minus a fluorescent signature indicating the presence of at least one target nucleic acid.

[0032] In some embodiments, optically illuminating the biological solution includes optically illuminating the biological solution using a light-emitting diode (LED) to emit light at a wavelength in a range of about 430 nm to about 500 nm.

[0033] In some embodiments, the detection of at least one fluorescent signature includes detecting at least one fluorescent signature without amplifying at least one fluorescent signature.

[0034] In some embodiments, the target nucleic acid is eukaryotic and / or prokaryotic.

[0035] In some modalities, the target nucleic acid is protozoan, bacterial, viral and / or fungal.

[0036] In some modalities, the target nucleic acid is from Chlamydia trachomatis, Neisseria gonorrhoeae, influenza A, influenza B, SARS-CoV-2, respiratory syncytial virus (RSV) and / or Trichomonas vaginalis.

[0037] In some embodiments, the detection of at least one fluorescent signature includes passing at least one fluorescent signature through a gel filter.

[0038] In another aspect, the present embodiments are directed to a method for detecting the presence of at least one target nucleic acid, the method including: obtaining a biological sample from a subject through a sample container; incubating the biological sample with at least one of a reagent and a buffer through the sample container, thereby producing a biological solution; inserting the sample container into a cartridge so that the biological solution flows into an internal chamber of the cartridge, the internal chamber including a first heating zone; inserting the cartridge into an electronic reader including multiple heating elements to create the Petition 870250102472, dated 10 / 11 / 2025, page 13 / 197 8 / 97 first heating zone and a second heating zone within the cartridge; perform a lysis step on the biological solution within the first heating zone; passively cool the biological solution by opening an internal passage of the cartridge so that the biological solution flows via gravity feed into the internal passage, the internal passage being fluidly downstream and vertically below the internal chamber; amplify one or more target nucleic acid(s) in the biological solution by isothermal amplification within the second heating zone comprising multiple reaction chambers fluidly downstream of the internal passage; wherein each of the multiple reaction chambers includes: a CRISPR / Cas enzyme with collateral cleavage activity; a guide RNA that hybridizes specifically with a target nucleic acid;and a detectably labeled nucleic acid probe, wherein hybridization of the guide RNA with the target nucleic acid induces or enhances the collateral cleavage activity of the CRISPR / Cas enzyme, and the CRISPR / Cas enzyme cleaves the detectably labeled nucleic acid probe, and wherein cleavage of the detectably labeled nucleic acid probe results in an increase in detectable labeling; illuminating the biological solution within each of the multiple reaction chambers through a plurality of optical energy sources, each energy source of the plurality of optical energy sources being disposed in the vicinity of one of the multiple reaction chambers; and determining the presence of at least one target nucleic acid within the biological solution based on the presence or level of the detectable label through a detection device.

[0039] In another aspect, the present embodiments are directed to a system for performing a nucleic acid diagnostic test, including: a durable electronic device capable of accepting a consumable cartridge; and the consumable cartridge configured to be Petition 870250102472, dated 10 / 11 / 2025, page 14 / 197 9 / 97 installed in the electronic device and including reagents used in the nucleic acid diagnostic test.

[0040] In some forms, the diagnostic test uses one or more reagents for CRISPR / Cas detection.

[0041] In some embodiments, two or more separate amplification reactions occur within the consumable cartridge.

[0042] In some forms, 8 amplification reactions occur within the consumable cartridge.

[0043] In some modalities, fluorescence detection is used to measure molecular amplification.

[0044] In some forms, excitation is used to aid fluorescence detection.

[0045] In some embodiments, optical filtration is used to assist in fluorescence detection.

[0046] In some embodiments, the thermal processing of the sample is conducted within the consumable cartridge.

[0047] In some embodiments, thermal lysis of the sample is conducted within the consumable cartridge.

[0048] In some modalities, gravity is used for fluidic motivation within the consumable cartridge.

[0049] In some embodiments, at least one result is displayed as a combination of: 1) indicator lights on the electronic device and 2) graphics on the consumable cartridge.

[0050] In some embodiments, the electronic device is configured to operate with various types of consumable cartridges.

[0051] In some models, the electronic device automatically detects the consumable cartridge configuration.

[0052] In some embodiments, the electronic device uses optical excitation and detection to determine whether a reaction chamber in the consumable cartridge contains a reagent. Petition 870250102472, dated 10 / 11 / 2025, page 15 / 197 10 / 97

[0053] In some modalities, the determination occurs in a continuous manner.

[0054] In some modes, the determination occurs in less than 1 second.

[0055] In some embodiments, the electronic device uses optical excitation and detection to determine whether a reaction chamber in the consumable cartridge contains a liquid.

[0056] In some forms, the liquid contains gas.

[0057] In some forms, the liquid includes a sample to be tested.

[0058] In some modalities, the determination occurs in a continuous manner.

[0059] In some modes, the determination occurs in less than 1 second.

[0060] In some embodiments, the electronic device uses optical excitation and detection to determine whether a reaction chamber contains a gas.

[0061] In another aspect, the present embodiments are directed to an electronic device for performing a nucleic acid diagnostic test in conjunction with a cartridge, the device including: an electronic subsystem that executes a test sequence based on pre-programmed parameters and unique parameters based on the type of cartridge installed; a mechanical subsystem that accepts and locates the cartridge; a thermal subsystem that heats two reaction zones within the cartridge; an optical subsystem that excites, filters, and detects fluorescence in real time; and a microfluidic control subsystem that triggers features on the cartridge to control fluid flow within the cartridge.

[0062] In some embodiments, the mechanical subsystem supports each of the following: the electronic subsystem, the thermal subsystem, the sub Petition 870250102472, dated 10 / 11 / 2025, page 16 / 197 11 / 97 optical system and microfluidic control subsystem.

[0063] In another aspect, the present embodiments are directed to a microfluidic cartridge for performing a nucleic acid diagnostic test in conjunction with an electronic device, the microfluidic cartridge including: an outer coating that interfaces with the electronic device; reagents contained within the coating; a fluidic valve that is actuated by the electronic device; filter elements that allow air to pass through the outer coating and retain liquids; and a visual indication that communicates identification information to the electronic device through at least one of absorbance and reflectance at predetermined locations.

[0064] In another aspect, the present embodiments are directed to a method of identifying a diagnostic cartridge, including: providing an apparatus for identifying a cartridge, the apparatus comprising: an optical module for measuring an optical signature within a first spectrum, wherein the optical module measures separate optical targets within the first spectrum to identify a cartridge type. In some embodiments, the optical module is configured to measure fluorescence in a second spectrum, the second spectrum being different from the first spectrum, the second spectrum to detect the presence, within the cartridge, of at least one nucleic acid from a predetermined group of nucleic acids, the predetermined group including nucleic acids that are each associated with one or more indications.

[0065] In some embodiments, the nucleic acid includes a human sample. In some embodiments, the cartridge includes one or more reagents for CRISPR / Cas detection.

[0066] In some embodiments, the cartridge includes an identification label comprising one or more optical targets. In some Petition 870250102472, dated 10 / 11 / 2025, p. 17 / 197 In 12 / 97 modes, the cartridge includes at least one printed barcode label.

[0067] In some embodiments, the method includes the use of a dual-mode photodetector to measure both the optical signature within the first spectrum and the fluorescence within the second spectrum. In some embodiments, the dual-mode photodetector uses two separate spectra enabled by two LEDs of different wavelengths. In some embodiments, the LEDs are computer-controlled.

[0068] In some embodiments, at least one printed barcode is ink printed (e.g., black ink, color ink, or a combination of inks).

[0069] In some embodiments, the optical targets include fluorescent ink including specific spectral properties.

[0070] In some embodiments, the method also comprises: inserting the cartridge into the device; illuminating the identification label by one of the two LEDs; detecting the optical signature associated with the optical signature; and identifying the cartridge type based on the detected optical signature.

[0071] In another aspect, the present embodiments are directed to a system including the reader and cartridge, as provided in this document.

[0072] In another aspect, the present embodiments are directed to a system for detecting the presence of a nucleic acid associated with at least one indication in a biological solution, the system including: an electronic reader for performing one or more assays and displaying the results thereof; a cartridge configured to be inserted into the reader, the cartridge including a cartridge assembly; and a sample collection container for collecting a biological sample and transferring it to an internal chamber of the cartridge. Petition 870250102472, dated 10 / 11 / 2025, page 18 / 197 13 / 97

[0073] In some embodiments, the system includes an internal assembly including the cartridge assembly once the cartridge is inserted into the reader, the internal assembly further including: a heating unit comprising one or more heating elements; and an optical assembly including at least one LED and at least one photodetector.

[0074] In some embodiments, the cartridge assembly includes a lysis chamber for receiving the biological sample from the sample collection container and one or more reaction chambers arranged fluidly downstream of the lysis chamber.

[0075] In some embodiments, one or more heating elements include a first heating element to maintain the lysis chamber at a first temperature and a second heating element to maintain one or more reaction chambers at a second temperature.

[0076] In some embodiments, the cartridge set includes: at least one buffer and reagent disposed within the lysis chamber; at least one lyophilized lysis bead disposed within the lysis chamber; and one lyophilized PCR bead disposed within each of the one or more reaction chambers.

[0077] In some embodiments, each of the one or more reaction chambers includes a transparent dome.

[0078] In some embodiments, the cartridge assembly includes a polymer shell forming a rear surface of the cartridge and a film layer including a front surface of the cartridge, the polymer shell and the film layer each sandwiching the buffer, reagent, at least one lyophilized lysis bead and / or lyophilized PCR bead between them.

[0079] In some embodiments, the film layer includes a polypropylene laminate. Petition 870250102472, dated 10 / 11 / 2025, p. 19 / 197 14 / 97

[0080] In some embodiments, at least one LED includes a first LED in optical communication with a reaction chamber of one or more reaction chambers and wherein at least one LED is configured to illuminate an interior of one or more reaction chambers.

[0081] In some embodiments, at least one LED includes a second LED in optical communication with at least one identification label arranged on a surface of the cartridge.

[0082] In some embodiments, at least one photodetector is configured to measure the fluorescence emitted from the illuminated interior of one or more reaction chambers.

[0083] In some embodiments, each of at least one LED and at least one photodetector is integrated into a printed circuit board assembly (PCBA).

[0084] In some embodiments, the heating unit is arranged adjacent to a front surface of the cartridge and the PCBA is arranged adjacent to a rear surface of the cartridge.

[0085] In some embodiments, the heating unit is integrated into the PCBA.

[0086] In some embodiments, one or more reaction chambers include multiple reaction chambers wherein one type of lyophilized PCR bead in a first reaction chamber of the multiple reaction chambers is different from one type of lyophilized PCR bead in a second reaction chamber of the multiple reaction chambers.

[0087] In some embodiments, one or more reaction chambers include multiple reaction chambers and each of the multiple reaction chambers includes a different type of lyophilized PCR bead configured to be used in a different reaction.

[0088] In some embodiments, one or more reaction chambers include multiple reaction chambers and each of the multiple chambers Petition 870250102472, dated 10 / 11 / 2025, page 20 / 197 15 / 97 reaction beads comprise the same type of lyophilized PCR bead configured for use in the same reaction.

[0089] In some embodiments, the light emitted from at least one LED excites at least one nucleic acid contained within one or more reaction chambers without passing through an optical lens.

[0090] In some embodiments, the system includes a mechanical assembly, wherein the mechanical assembly is configured to move the cartridge laterally within the reader after the cartridge is inserted into the reader, by means of closing a reader cover, the mechanical assembly comprising: at least one linkage coupling the cover to an internal device disposed within the reader; and a cam coupled to at least one linkage and to the internal device, the cam converting the closing motion of the cover into lateral movement of the internal device.

[0091] In some embodiments, the cartridge includes at least one identification mark configured to be illuminated by at least one LED. In some embodiments, at least one identification mark includes at least one printed barcode. In some embodiments, at least one identification mark includes one or more printed shapes. In some embodiments, at least one identification mark is printed in ink (e.g., black ink, color ink, or a combination of inks). In some embodiments, at least one identification mark is associated with at least one indication.

[0092] In some respects, the present disclosure provides an in vitro detection system based on CRISPR. The exemplary detection system is shown in Figure 1. In some respects, the present disclosure provides a sample collection. In some respects, a sample collection includes a sterile swab and a container. Petition 870250102472, dated 10 / 11 / 2025, page 21 / 197 16 / 97 buffer / reagent. In some respects, the present disclosure provides a cartridge. In some respects, a cartridge is disposable. In some respects, the present disclosure provides a reader. In some respects, a reader is a powered reader. In some respects, a powered reader is a USB-powered processing device. In some respects, the powered reader may be battery-powered.

[0093] A diagnostic device, as provided in this document, provides an accurate and easy-to-use home test to detect a target nucleic acid, for example, pathogens such as viruses or bacteria, in a device that is designed for multiplex detection. An exemplary in vitro diagnostic system is a molecular test for COVID / Flu multiplex with a nasal swab sample. Another exemplary in vitro test is a molecular test for a Sexually Transmitted Infection (STI) panel including a multiplex positive and negative control result using a genital (e.g., vaginal) swab.

[0094] These disclosures include detection devices and methods for detecting one or more target nucleic acids with distinct advantages over currently available diagnostic testing products, including but not limited to: molecular test accuracy enhanced by CRISPR technology; sensitivity and selectivity equivalent to laboratory-based PCR testing; multiplex capability where a single sample can perform multiple assays (e.g., 8 separate chambers available for assay and control reactions); menu expandability, with rapid assay and test kit development; two programmable heating zones (e.g., thermal lysis is performed separately from amplification reactions); a durable, low-cost player designed for home use; no calibration or maintenance required; and operation of Petition 870250102472, dated 10 / 11 / 2025, p. 22 / 197 17 / 97 low cost provided by microfluidic gravity flow. Furthermore, the devices and detection methods of the present disclosure are easy to use. The systems of the present disclosure run from start to finish without user intervention during the test sequences.

[0095] These disclosures also provide cartridges. In some respects, a cartridge is suitable for use in a detection system according to these disclosures. In some respects, a cartridge is configured for a reader, as provided in this document.A cartridge according to the present disclosures provides a number of advantages, including, but not limited to: reagent cartridge identification with very low-cost components; the barcode reader can read barcodes using only 4 additional LED components; software and photodetector components are shared to provide dual purposes; spectral encoding of label cartridge ID targets is visible to the common photodetector through selective LED wavelength excitation, preserving a fluorescence measurement channel with the same photodetector; and unique label ID patterns provide static and dynamic detection modes as well as position information. BRIEF DESCRIPTION OF THE DRAWINGS

[0096] Figure 1A illustrates a sample collection container of an in vitro diagnostic testing platform, according to aspects of the present embodiments.

[0097] Figure 1B illustrates an in vitro diagnostic test platform cartridge, according to aspects of the present embodiments.

[0098] Figure 1C illustrates a reader of an in vitro diagnostic testing platform, according to aspects of the present modality Petition 870250102472, dated 10 / 11 / 2025, p. 23 / 197 18 / 97 des.

[0099] Figure 1D illustrates a sample collection container inserted into a cartridge, which is then inserted into a reader of an in vitro diagnostic testing platform, according to aspects of the present embodiments.

[00100] Figure 1E illustrates an exemplary detection device system of an in vitro diagnostic testing platform, according to aspects of the present embodiments.

[00101] Figure 2A illustrates a positive reader outcome indicator, according to aspects of the present modalities.

[00102] Figure 2B illustrates a negative reader outcome indicator, according to aspects of the present modalities.

[00103] Figure 3 illustrates a combined summary of the user workflow and the test workflow, according to aspects of the present modalities.

[00104] Figure 4A illustrates a nasal swab collection, according to aspects of the present modalities.

[00105] Figure 4B illustrates the elution of a sample in a buffer in a sample collection container, according to aspects of the present embodiments.

[00106] Figure 5 illustrates a sample transfer to a cartridge, according to aspects of the present embodiments.

[00107] Figure 6 illustrates the installation of the cartridge, according to aspects of the present embodiments.

[00108] Figure 7 illustrates LEDs indicating the reader's status, according to aspects of the present embodiments.

[00109] Figure 8A illustrates cartridge lysis heating, according to aspects of the present embodiments.

[00110] Figure 8B illustrates the thermal control of lysis in cross-sectional view, according to aspects of the present embodiments. Petition 870250102472, dated 10 / 11 / 2025, p. 24 / 197 19 / 97

[00111] Figure 9 illustrates the transfer of a biological solution to reaction chambers, according to aspects of the present embodiments.

[00112] Figure 10A illustrates the heating of the reaction chamber in cross-sectional view, according to aspects of the present embodiments.

[00113] Figure 10B illustrates the thermal control of the reaction chamber in cross-sectional view, according to aspects of the present embodiments.

[00114] Figure 11A illustrates exemplary LAMP curves including Targeted SARS Cov-2 Assay, according to aspects of the present embodiments.

[00115] Figure 11B illustrates exemplary LAMP curves including negative control, according to aspects of the present embodiments.

[00116] Figure 12 illustrates a model summary of exemplary execution, according to aspects of the present modalities.

[00117] Figure 13 illustrates a reader fixation mechanism in an open position, in perspective view (left) and side view (right), according to aspects of the present embodiments.

[00118] Figure 14 illustrates a reader fixation mechanism in a closed position, in perspective view (left) and side view (right), according to aspects of the present embodiments.

[00119] Figure 15A illustrates an optical module including an optical printed circuit board (PCBA) assembly according to aspects of the present embodiments.

[00120] Figure 15B illustrates an optical module including an optical printed circuit board (PCBA) assembly overlaid with an inserted cartridge, according to aspects of the present embodiments. Petition 870250102472, dated 10 / 11 / 2025, p. 25 / 197 20 / 97

[00121] Figure 16 illustrates a blue LED emission spectrum, according to aspects of the present embodiments.

[00122] Figure 17 illustrates fluorescein emission and excitation spectra, according to aspects of the present embodiments.

[00123] Figure 18 illustrates a transmission spectrum for a Kodak Wratten 2-12 optical filter, according to aspects of the present embodiments.

[00124] Figure 19A illustrates an optical PCBA with photodiodes, according to aspects of the present embodiments.

[00125] Figure 19B illustrates an optical PCBA with phototransistors, according to aspects of the present embodiments.

[00126] Figure 20A illustrates heater temperature profiles for the lysis chamber, according to aspects of the present embodiments.

[00127] Figure 20B illustrates heater temperature profiles for the reaction chamber, according to aspects of the present embodiments.

[00128] Figure 21 illustrates temperature profiles for multiple reaction chambers, according to aspects of the present embodiments.

[00129] Figure 22 illustrates a sequence of operation of the basic system, according to aspects of the present modalities.

[00130] Figure 23A illustrates system timing diagrams for the global system, according to aspects of the present embodiments.

[00131] Figure 23B illustrates system timing diagrams for the cartridge ID sequence, according to aspects of the present embodiments.

[00132] Figure 24A illustrates a system timing diagram for a cartridge ID sequence in high-speed mode. Petition 870250102472, dated 10 / 11 / 2025, page 26 / 197 21 / 97 age (A), in accordance with aspects of the present modalities.

[00133] Figure 24B illustrates a system timing diagram for a fill detection algorithm sequence, according to aspects of the present embodiments.

[00134] Figure 25A illustrates a system timing diagram for LAMP (A) fluorescence measurement timing, according to aspects of the present embodiments.

[00135] Figure 25B illustrates a system timing diagram for a detailed A / D timing of LAMP fluorescence measurement, according to aspects of the present embodiments.

[00136] Figure 26 illustrates details of the cartridge assembly in cross-sectional view, according to aspects of the present embodiments.

[00137] Figure 27 illustrates details of the cartridge assembly in exploded perspective view, according to aspects of the present embodiments.

[00138] Figure 28A illustrates details of the static cartridge identification characteristics, according to aspects of the present embodiments.

[00139] Figure 28B illustrates details of the static cartridge identification characteristics, according to aspects of the present embodiments.

[00140] Figure 28C illustrates details of the static cartridge identification characteristics, according to aspects of the present embodiments.

[00141] Figure 28D illustrates details of the static cartridge identification characteristics, according to aspects of the present embodiments.

[00142] Figure 29 illustrates details of a respiratory cartridge panel, according to aspects of the present embodiments. Petition 870250102472, dated 10 / 11 / 2025, page 27 / 197 22 / 97

[00143] Figure 30 illustrates details of an STI cartridge panel, according to aspects of the present embodiments.

[00144] Figure 31 illustrates details of the LED circuit, according to aspects of the present embodiments.

[00145] Figure 32 illustrates a cartridge panel with ambient light blocking color, in accordance with aspects of the present embodiments.

[00146] Figure 33 illustrates an exemplary LED emission spectrum, according to aspects of the present embodiments.

[00147] Figure 34 illustrates an exemplary LED emission spectrum, in accordance with aspects of the present embodiments.

[00148] Figure 35 illustrates a cross-sectional side view of the reaction chamber assembly according to aspects of the present embodiments.

[00149] Figure 36 illustrates an enlarged cross-sectional side view of the reaction chamber assembly according to aspects of the present embodiments.

[00150] Figure 37 illustrates a method for detecting viruses, according to aspects of the present embodiments.

[00151] Figure 38 illustrates a cartridge identification method, according to aspects of the present embodiments.

[00152] Figure 39 illustrates a method for detecting fill, according to aspects of the present modalities.

[00153] Figure 40 illustrates a LAMP fluorescence measurement timing sequence, according to aspects of the present embodiments.

[00154] Figure 41A illustrates an exemplary industrial design concept, in accordance with aspects of the present modalities.

[00155] Figure 41B illustrates an exemplary industrial design concept, in accordance with aspects of the present modalities. Petition 870250102472, dated 10 / 11 / 2025, page 28 / 197 23 / 97

[00156] Figure 41C illustrates an exemplary industrial design concept, in accordance with aspects of the present embodiments.

[00157] Figure 41D illustrates an exemplary industrial design concept, in accordance with aspects of the present embodiments.

[00158] Figure 41E illustrates an exemplary industrial design concept, in accordance with aspects of the present embodiments.

[00159] Figure 41F illustrates an exemplary industrial design concept, in accordance with aspects of the present embodiments.

[00160] Figure 42A illustrates an alternative user workflow concept, in accordance with aspects of the present modalities.

[00161] Figure 42B illustrates an alternative user workflow concept, according to aspects of the present modalities.

[00162] Figure 42C illustrates an alternative user workflow concept, in accordance with aspects of the present modalities.

[00163] Figure 43 illustrates a cross-sectional side view of the reaction chamber assembly in an alternative configuration, according to aspects of the present embodiments. DEFINITIONS

[00164] Ambient temperature: As used in this document, the term ambient temperature is the temperature of the environment. In general, the term ambient temperature should be understood as the temperature of any object or environment surrounding an item. Measuring an ambient temperature can be done using a thermometer or sensor. The ambient temperature of an item depends on the temperature of the item's environment. The environment can have any temperature, such as a temperature below 95°C, such as below 90°C, such as below 85°C, such as below 80°C, such Petition 870250102472, dated 10 / 11 / 2025, page 29 / 197 24 / 97 as below 75°C, such as below 70°C, such as below 65°C, such as below 60°C, such as below 55°C, such as below 50°C, such as below 45°C, such as below 40°C, such as below 35°C, such as below 30°C, such as below 25°C, such as below 24°C, such as below 23°C, such as below 22°C, such as below 21°C, such as below 20°C. Examples of ambient temperature ranges include 5°C to 50°C, such as 10°C to 40°C, such as 15°C to 35°C, such as 20°C to 30°C, such as 20°C to 25°C, such as 20°C to 22°C.

[00165] Biological Sample: As used in this document, the term biological sample typically refers to a sample obtained or derived from a biological source (e.g., a tissue or organism or cell culture) of interest, as described in this document. In some embodiments, a source of interest is or comprises an organism, such as an animal or human. In some embodiments, a biological sample is or comprises biological tissue or fluid.In some embodiments, a biological sample may be or comprise bone marrow; blood; blood cells; ascites; tissue or fine-needle biopsy samples; body fluids containing cells; free-floating nucleic acids; sputum; saliva; urine; cerebrospinal fluid; peritoneal fluid; pleural fluid; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washings or rinses, such as ductal washes or bronchoalveolar washes; aspirates; scrapings; bone marrow specimens; tissue biopsy specimens; surgical specimens; other body fluids, secretions and / or excretions; and / or cells thereof and / or combinations or components thereof, etc. In some embodiments, a biological sample is or comprises cells obtained from an individual. In some embodiments, the cells obtained are or include cells from an individual from whom the sample is taken. Petition 870250102472, dated 10 / 11 / 2025, page 30 / 19725 / 97 obtained. In some embodiments, a sample is a primary sample obtained directly from a source of interest by any appropriate means. For example, in some embodiments, a primary biological sample is obtained by methods selected from the group consisting of biopsy (e.g., fine needle aspiration or tissue biopsy), surgery, collection of body fluid (e.g., blood, lymph, feces, etc.), etc. In some embodiments, as will become evident from the context, the term sample refers to a preparation that is obtained by processing (e.g., removing one or more components from and / or adding one or more agents to) a primary sample. For example, filtration using a semipermeable membrane may be used.Such a processed sample may comprise, for example, nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to techniques such as mRNA amplification or reverse transcription, isolation and / or purification of certain components, etc.

[00166] Cell Lysate: As used in this document, the term cell lysate or cell lysate refers to a fluid containing the contents of one or more ruptured cells (i.e., cells whose membrane has been ruptured). In some embodiments, a cell lysate includes both hydrophilic and hydrophobic cellular components. In some embodiments, a cell lysate includes predominantly hydrophilic components; in some embodiments, a cell lysate includes predominantly hydrophobic components. In some embodiments, a cell lysate is a lysate of one or more cells selected from the group consisting of plant cells, microbial cells (e.g., bacterial or fungal), animal cells (e.g., mammalian cells), human cells, and combinations thereof. In some embodiments, a cell lysate is a lysate of one or more abnormal cells, such as cancerous cells. In some embodiments, Petition 870250102472, dated 10 / 11 / 2025, page 31 / 197 26 / 97 A cell lysate is a crude lysate in which little or no purification is performed after cell disruption; in some embodiments, such a lysate is referred to as a primary lysate. In some embodiments, one or more isolation or purification steps are performed on a primary lysate; however, the term lysate refers to a preparation that includes multiple cellular components and not to pure preparations of any single component.

[00167] Composition: Those skilled in the art will appreciate that the term composition, as used in this document, can be used to refer to a discrete physical entity comprising one or more specified components. In general, unless otherwise specified, a composition can be of any form (e.g., gas, gel, liquid, solid, etc.) or combination of forms.

[00168] Complementary: As used in this document, the term complementary refers to the general relationship between polymeric molecules, for example, between polynucleotides. In some embodiments, polynucleotides, such as nucleotide sequences (e.g., initiator nucleotide sequences or target nucleotide sequences), are considered complementary to each other if their sequences are at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% identical. In some embodiments, polynucleotides are considered complementary to each other if their sequences are at least 80%, at least 85%, at least 90%, at least 95%, at least 99%, or 100% similar. In some embodiments, polynucleotides are considered complementary to each other if they are capable of hybridizing with each other.

[00169] Comprising: A composition or method described in this document as comprising one or more named elements or steps is open-ended, meaning that the named elements or steps are essential, but other elements or steps may be included. Petition 870250102472, dated 10 / 11 / 2025, page 32 / 197 27 / 97 may be added within the scope of the composition or method. To avoid verbosity, it is also understood that any composition or method described as comprising (or including) one or more named elements or steps also describes the corresponding and more limited composition or method consisting essentially of (or consisting essentially of) the same named elements or steps, meaning that the composition or method includes the essential named elements or steps and may also include additional elements or steps that do not materially affect the basic and novel feature(s) of the composition or method.It is also understood that any composition or method described in this document as comprising or consisting essentially of one or more named elements or steps also describes the corresponding, more limited and closed composition or method consisting of (or consisting of) the named elements or steps to the exclusion of any other unnamed element or step. In any composition or method disclosed in this document, known or disclosed equivalents of any named essential element or step may be substituted for that element or step.

[00170] Detectable entity: The term detectable entity, as used in this document, refers to any element, molecule, functional group, compound, fragment, or fraction that is detectable. In some embodiments, a detectable entity is provided or used alone. In some embodiments, a detectable entity is provided and / or used in association with (e.g., bonded to) another agent. Examples of detectable entities include, but are not limited to: various ligands, radionuclides (e.g., 3H, 14C, 18F, 19F, 32P, 35S, 135I, 125I, 123I, 64Cu, 187Re, 111In, 90Y, 99mTc, 177Lu, 89Zr, etc.), fluorescent dyes (for example, fluorescent dyes). Petition 870250102472, dated 10 / 11 / 2025, p. 33 / 197 28 / 97 specific markers, see below), chemiluminescent agents (such as, for example, acridinum esters, stabilized dioxetanes, and the like), bioluminescent agents, spectrally resolvable inorganic fluorescent semiconductor nanocrystals (i.e., quantum dots), metal nanoparticles (e.g., gold, silver, copper, platinum, etc.), nanoclusters, paramagnetic metal ions, enzymes (for specific examples of enzymes, see below), colorimetric labels (such as, for example, dyes, colloidal gold, and the like), biotin, dioxygenin, haptens, and proteins for which anti-serum or monoclonal antibodies are available.

[00171] Determination: Many methodologies described in this document include a determination step. Those skilled in the art, reading this descriptive report, will appreciate that such determination may utilize or be performed using any of a variety of techniques available to those skilled in the art, including, for example, specific techniques explicitly referred to in this document. In some embodiments, the determination involves the manipulation of a physical sample. In some embodiments, the determination involves consideration and / or manipulation of data or information, for example, using a computer or other processing unit adapted to perform a relevant analysis. In some embodiments, the determination involves receiving relevant information, data, and / or materials from a source. In some embodiments, the determination involves comparing one or more characteristics of a sample or entity with a comparable reference.

[00172] Diagnostic information: As used in this document, diagnostic information or information for use in diagnosis is information useful for determining whether a patient has a disease, disorder or condition and / or for classifying a of Petition 870250102472, dated 10 / 11 / 2025, page 34 / 197 29 / 97 disease, disorder, or condition in a phenotypic category or any category with significance regarding the prognosis of a disease, disorder, or condition, or probable response to treatment (treatment in general or any specific treatment) of a disease, disorder, or condition. Similarly, diagnosis refers to providing any type of diagnostic information, including, but not limited to, whether a subject is likely to have or develop a disease, disorder, or condition, the state, staging, or characteristic of a disease, disorder, or condition manifested in the subject, information relating to the nature or classification of a tumor, information relating to prognosis, and / or information useful in selecting an appropriate treatment. Treatment selection may include choosing a specific therapeutic agent or other treatment modality, such as surgery, radiation, etc., a choice about withholding or administering therapy, a choice related to the dosage regimen (e.g., frequency or level of one or more doses of a specific therapeutic agent or combination of therapeutic agents), etc.

[00173] Gel: As used herein, the term gel refers to viscoelastic materials whose rheological properties distinguish them from solutions, solids, etc. In some embodiments, a composition is considered a gel if its storage modulus (G') is greater than its modulus (G). In some embodiments, a composition is considered a gel if there are chemical or physical cross-linked networks in solution, which is distinguished from entangled molecules in viscous solution.

[00174] In vitro: The term in vitro, as used in this document, refers to events that occur in an artificial environment, for example, in a test tube or reaction vessel, in cell culture, etc., rather than within a multicellular organism. Petition 870250102472, dated 10 / 11 / 2025, p. 35 / 197 30 / 97

[00175] Isolate: As used in this document, the term isolate refers to a substance and / or entity that has been (1) separated from at least some of the components with which it was associated when initially produced (either in nature and / or in an experimental setting) and / or (2) designed, produced, prepared and / or manufactured by human hands. Isolated substances and / or entities may be separated from about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or more than about 99% of the other components with which they were initially associated. In some embodiments, the isolated agents are approximately 80%, approximately 85%, approximately 90%, approximately 91%, approximately 92%, approximately 93%, approximately 94%, approximately 95%, approximately 96%, approximately 97%, approximately 98%, approximately 99% or more than approximately 99% pure.As used in this document, a substance is pure if it is substantially free of other components. In some embodiments, as will be understood by those skilled in the art, a substance may still be considered isolated or even pure after it has been combined with certain other components, such as, for example, one or more carriers or excipients (e.g., buffer, solvent, water, etc.); in such embodiments, the percentage of isolation or purity of the substance is calculated without including such carriers or excipients. To give just one example, in some embodiments, a biological polymer, such as a polypeptide or polynucleotide that occurs in nature, is considered isolated when, a) by virtue of its origin or source of derivation, it is not associated with some or all of the components that accompany it in its native state in nature; b) it is substantially free of other polypeptides or nucleic acids of the same nature. Petition 870250102472, dated 10 / 11 / 2025, page 36 / 197 31 / 97 species of the species that produces it in nature; or c) is expressed by or is otherwise associated with components of a cell or other expression system that is not of the species that produces it in nature. Thus, for example, in some embodiments, a polypeptide that is chemically synthesized or is synthesized in a cellular system different from that which produces it in nature is considered an isolated polypeptide. Alternatively or additionally, in some embodiments, a polypeptide that has been subjected to one or more purification techniques may be considered an isolated polypeptide insofar as it has been separated from other components a) with which it is associated in nature; and / or b) with which it was associated when initially produced.

[00176] Nucleic acid: As used herein, in its broadest sense, the term nucleic acid refers to any compound and / or substance that is or can be incorporated into an oligonucleotide chain. In some embodiments, a nucleic acid is a compound and / or substance that is or can be incorporated into an oligonucleotide chain via a phosphodiester bond. As will become clear from the context, in some embodiments, nucleic acid refers to an individual nucleic acid residue (e.g., a nucleotide and / or nucleoside); in some embodiments, nucleic acid refers to a chain of oligonucleotides comprising individual nucleic acid residues. In some embodiments, a nucleic acid is or comprises RNA; in some embodiments, a nucleic acid is or comprises DNA. In some embodiments, a nucleic acid is, comprises, or consists of one or more natural nucleic acid residues.In some embodiments, a nucleic acid is, comprises, or consists of one or more nucleic acid analogs. In some embodiments, a nucleic acid analog differs from a nucleic acid in that it does not utilize a major structure of the same. Petition 870250102472, dated 10 / 11 / 2025, p. 37 / 197 32 / 97 phosphodiester. For example, in some embodiments, a nucleic acid is, comprises, or consists of one or more peptide nucleic acids, which are known in the art and have peptide linkages instead of phosphodiester linkages in the back chain, and are considered within the scope of the systems and / or methods provided in this document. Alternatively or additionally, in some embodiments, a nucleic acid has one or more phosphorothioate and / or 5'-N-phosphoramidite linkages instead of phosphodiester linkages. In some embodiments, a nucleic acid is, comprises, or consists of one or more natural nucleosides (e.g., adenosine, thymidine, guanosine, cytidine, uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine).In some embodiments, a nucleic acid is, comprises, or consists of one or more nucleoside analogs (for example, 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolopyrimidine, 3-methyladenosine, 5-methylcytidine, C-5 propynylcytidine, C-5 propynyluridine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyluridine, C5-propynylcytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, 2-thiocytidine, methylated bases, intercalated bases, and combinations thereof). In some embodiments, a nucleic acid comprises one or more modified sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose) compared to those in natural nucleic acids. In some embodiments, a nucleic acid has a nucleotide sequence that encodes a functional gene product, such as an RNA or protein.In some embodiments, a nucleic acid includes one or more introns. In some embodiments, nucleic acids are prepared by one or more of the following: isolation from a natural source, enzymatic synthesis by polymerization based on a complementary model (in vivo or in vitro), reproduction in a cell. Petition 870250102472, dated 10 / 11 / 2025, p. 38 / 197 33 / 97 or recombinant system and chemical synthesis. In some forms, a nucleic acid is at least 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000 or more residues in length. In some embodiments, a nucleic acid is partially or entirely single-stranded; in some embodiments, a nucleic acid is partially or entirely double-stranded. In some embodiments, a nucleic acid has a nucleotide sequence comprising at least one coding element, or is the complement of a coding sequence, a polypeptide. In some embodiments, a nucleic acid has enzymatic activity.

[00177] Pandemic strain: A pandemic influenza strain is one that has or has the capacity to cause pandemic infection in human populations. In some embodiments, a pandemic strain has caused pandemic infection. In some embodiments, such pandemic infection involves epidemic infection in multiple territories and, particularly, in territories separated from one another (e.g., by mountains, bodies of water, as part of distinct continents, etc.), so that infections do not normally pass between them.

[00178] Prognostic and predictive information: As used in this document, the terms prognostic and predictive information refer to any information that can be used to indicate any aspect of the course of a disease or condition, whether in the absence or presence of treatment. Such information may include, but is not limited to, a patient's average life expectancy, the probability that a patient will survive for a given period of time (e.g., 6 months, 1 year, 5 years, etc.), the probability that a patient Petition 870250102472, dated 10 / 11 / 2025, page 39 / 197 34 / 97 being cured of a disease, the probability that a patient's disease will respond to a specific therapy (where response can be defined in various ways). Prognostic and predictive information is included in the broad category of diagnostic information.

[00179] Polypeptide: As used in this document, refers to any polymeric chain of amino acids. In some embodiments, a polypeptide has an amino acid sequence that occurs in nature. In some embodiments, a polypeptide has an amino acid sequence that does not occur in nature. In some embodiments, a polypeptide has an amino acid sequence that is manipulated to the extent that it is designed and / or produced through the action of human hands. In some embodiments, a polypeptide may comprise or consist of natural amino acids, non-natural amino acids, or both. In some embodiments, a polypeptide may comprise or consist only of natural amino acids or only non-natural amino acids. In some embodiments, a polypeptide may comprise D-amino acids, L-amino acids, or both. In some embodiments, a polypeptide may comprise only D-amino acids. In some embodiments, a polypeptide may comprise only L-amino acids.In some embodiments, a polypeptide may include one or more pendant groups or other modifications, for example, modifying or attaching to one or more amino acid side chains, at the N-terminus of the polypeptide, at the C-terminus of the polypeptide, or any combination thereof. In some embodiments, such pendant groups or modifications may be selected from the group consisting of acetylation, amidation, lipidation, methylation, pegylation, etc., including combinations thereof. In some embodiments, a polypeptide may be cyclic and / or may comprise a cyclic portion. In some embodiments, a... Petition 870250102472, dated 10 / 11 / 2025, p. 40 / 197 35 / 97 A polypeptide is not cyclic and / or does not comprise any cyclic portion. In some embodiments, a polypeptide is linear. In some embodiments, a polypeptide may be or comprise a stapled polypeptide. In some embodiments, the term polypeptide may be appended to a reference polypeptide name, activity, or structure; in such cases, it is used in this document to refer to polypeptides that share the relevant activity or structure and therefore may be considered members of the same polypeptide class or family. For each of these classes, this descriptive report provides, and / or those skilled in the art will be aware of, exemplary polypeptides within the class whose amino acid sequences and / or functions are known; in some embodiments, such exemplary polypeptides are reference polypeptides for the polypeptide class or family.In some embodiments, a member of a polypeptide class or family shows significant sequence homology or identity with, shares a common sequence motif (e.g., a characteristic sequence element) with, and / or shares common activity (in some embodiments at a comparable level or within a designated range) with a reference polypeptide of the class; in some embodiments with all polypeptides within the class.For example, in some embodiments, a member polypeptide shows an overall degree of homology or sequence identity with a reference polypeptide that is at least about 30-40% and is often greater than about 50%, 60%, 70%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more and / or includes at least one region (e.g., a conserved region that may, in some embodiments, be or comprise a characteristic sequence element) that shows very high sequence identity, often greater than 90% or even 95%, 96%, 97%, 98% or 99%. Such a region... Petition 870250102472, dated 10 / 11 / 2025, p. 41 / 197 A conserved 36 / 97 region typically spans at least 3-4 and often up to 20 or more amino acids; in some embodiments, a conserved region spans at least a stretch of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids. In some embodiments, a relevant polypeptide may comprise or consist of a fragment of a parental polypeptide.In some embodiments, a useful polypeptide may comprise or consist of a plurality of fragments, each of which is found in the same precursor polypeptide in a different spatial arrangement relative to each other than is found in the polypeptide of interest (e.g., fragments that are directly linked in the precursor may be spatially separated in the polypeptide of interest or vice versa, and / or fragments may be present in a different order in the polypeptide of interest than in the precursor), such that the polypeptide of interest is a derivative of its precursor polypeptide.

[00180] Protein: As used in this document, the term protein refers to a polypeptide (i.e., a sequence of at least two amino acids linked together by peptide bonds). Proteins may include different fractions of amino acids (e.g., they may be glycoproteins, proteoglycans, etc.) and / or may be otherwise processed or modified. Those skilled in the art will appreciate that a protein may be a complete polypeptide chain as produced by a cell (with or without a signal sequence), or it may be a characteristic portion thereof. Those skilled in the art will appreciate that a protein may sometimes include more than one polypeptide chain, for example, linked by one or more disulfide bonds or associated by other means. Polypeptides may contain L-amino acids, D-amino acids, or both, and may contain any of a variety of amino acid modifications or Petition 870250102472, dated 10 / 11 / 2025, page 42 / 197 37 / 97 known analogues in the art. Useful modifications include, for example, terminal acetylation, amidation, methylation, etc. In some embodiments, proteins may comprise natural amino acids, non-natural amino acids, synthetic amino acids, and combinations thereof. The term peptide is generally used to refer to a polypeptide with a length of less than about 100 amino acids, less than about 50 amino acids, less than 20 amino acids, or less than 10 amino acids. In some embodiments, proteins are antibodies, antibody fragments, biologically active portions thereof, and / or characteristic portions thereof.

[00181] Reference: As used in this document, describes a standard or control against which a comparison is made. For example, in some embodiments, an agent, animal, individual, population, sample, sequence, or value of interest is compared with a reference or control agent, animal, individual, population, sample, sequence, or value. In some embodiments, a reference or control is tested and / or determined substantially simultaneously with the test or determination of interest. In some embodiments, a reference or control is a historical reference or control, optionally embodied in a tangible medium. Typically, as would be understood by those skilled in the art, a reference or control is determined or characterized under conditions or circumstances comparable to those under evaluation.Those skilled in the art will appreciate it when sufficient similarities are present to justify reliance on and / or comparison with a particular possible reference or control.

[00182] Sample: As used herein, the term sample typically refers to an aliquot of material obtained or derived from a source of interest, as described herein. In some embodiments, a source of interest is a biological or environmental source. In some embodiments, a source of interest is a biological or environmental source. Petition 870250102472, dated 10 / 11 / 2025, p. 43 / 197 38 / 97 but embodiments, a source of interest may be or comprise a cell or an organism, such as a microbe, a plant, or an animal (e.g., a human being). In some embodiments, a source of interest is or comprises biological tissue or fluid. In some embodiments, a biological tissue or fluid may be or comprise amniotic fluid, aqueous humor, ascites, bile, bone marrow, blood, breast milk, cerebrospinal fluid, cerumen, chyle, chorionic goosebumps, ejaculate, endolymph, exudate, feces, gastric acid, gastric juice, lymph, mucus, pericardial fluid, perilymph, peritoneal fluid, pleural fluid, pus, rheumatism, saliva, sebum, semen, serum, smegma, expectoration, synovial fluid, sweat, tears, urine, vaginal secretions, vitreous humor, vomit, and / or combinations or components thereof.In some embodiments, a biological fluid may be or comprise an intracellular fluid, an extracellular fluid, an intravascular fluid (blood plasma), an interstitial fluid, a lymphatic fluid, and / or a transcellular fluid. In some embodiments, a biological fluid may be or comprise a plant exudate. In some embodiments, a biological tissue or sample may be obtained, for example, by aspiration, biopsy (e.g., fine needle or tissue biopsy), swab (e.g., oral, nasal, skin, or vaginal swab), scraping, surgery, wash, or flush (e.g., bronchoalveolar, ductal, nasal, ocular, oral, uterine, vaginal, or other wash). In some embodiments, a biological sample is or comprises cells obtained from an individual. In some embodiments, a sample is a primary sample obtained directly from a source of interest by any appropriate means.In some embodiments, as will become clear from the context, the term sample refers to a preparation that is obtained by processing (e.g., removing one or more components from and / or adding one or more agents to) a primary sample. For example, filtration using a semi-membrane. Petition 870250102472, dated 10 / 11 / 2025, page 44 / 197 Permeable 39 / 97 can be used. Such a processed sample may comprise, for example, nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to one or more techniques, such as nucleic acid amplification or reverse transcription, isolation and / or purification of certain components, etc.

[00183] Specificity: As is known in the art, specificity is a measure of the ability of a particular ligand to distinguish its binding partner from other potential binding partners.

[00184] Static: As used in this document, the term static in the context of cartridge identification specifies that the cartridge ID process is performed after a cartridge is fully inserted into the reader and / or that the cartridge ID process occurs when the cartridge is not being moved.

[00185] Subject: As used in this document, the term subject refers to an organism, for example, a mammal (e.g., a human being, a non-human mammal, a non-human primate, a primate, a laboratory animal, a mouse, a rat, a hamster, a gerbil, a cat, a dog). In some embodiments, a human subject is an adult, adolescent, or pediatric subject. In some embodiments, a subject has a disease, disorder, or condition, for example, a disease, disorder, or condition that can be treated as provided in this document, for example, a cancer or a tumor listed in this document. In some embodiments, a subject is susceptible to a disease, disorder, or condition; in some embodiments, a susceptible subject is predisposed to and / or shows an increased risk (compared to the average risk observed in a reference subject or population) of developing the disease, disorder, or condition.In some forms, a subject exhibits one or more symptoms of a disease, disorder, or condition. Petition 870250102472, dated 10 / 11 / 2025, page 45 / 197 40 / 97 In some modalities, a subject does not exhibit a particular symptom (e.g., clinical manifestation of the disease) or characteristic of a disease, disorder, or condition. In some modalities, a subject does not exhibit any symptoms or characteristics of a disease, disorder, or condition. In some modalities, a subject is a patient. In some modalities, a subject is an individual to whom diagnosis and / or therapy is and / or has been administered. DETAILED DESCRIPTION OF CERTAIN MODALITIES

[00186] In some embodiments, the present disclosure provides readers, cartridges, sample collection devices, detection systems and methods for detecting one or more target nucleic acids. A. Reader and Essay Workflow

[00187] Figure 1A illustrates a sample collection container 18, lid 20, and swab 16 of an in vitro diagnostic testing platform, according to aspects of the present embodiments. Figure 1B illustrates a cartridge 12 of an in vitro diagnostic testing platform, according to aspects of the present embodiments. Figure 1C illustrates a reader 14 of an in vitro diagnostic testing platform, according to aspects of the present embodiments. Figure 1D illustrates a sample collection container inserted into a cartridge, which is then inserted into a reader of an in vitro diagnostic testing platform, according to aspects of the present embodiments. Figure 1E illustrates an exemplary detection device system 10 of an in vitro diagnostic testing platform, including a sample collection container 18, a cartridge 12, and a reader 14, according to aspects of the present embodiments.

[00188] In some embodiments, the present disclosure provides a reader 14. In some embodiments, a reader is a powered reader 14. In some respects, a powered reader is a USB-powered processing device. As shown in Fig. 1, a Petition 870250102472, dated 10 / 11 / 2025, page 46 / 197 41 / 97 reader 14 may be part of a system 10 (shown in Figure 1D). A reader is a device that is intended to be very easy to use with simple workflows that a lay (non-professional) user can use adequately without formal training. The system 10 may include the reader 14 (shown in Figure 1C), a swab 16 to obtain a biological sample (e.g., saliva, mucus, nasal swab, oral swab, etc.), a fluid container / bottle / reservoir 18 to receive the sample, a cap 20 to fluidly close the fluid container / bottle / reservoir 18 (all shown in Figure 1A), and a cartridge 12 shown in Figure 1B. As shown in Figure 1C, the reader 14 may include a slot 22 to receive the cartridge 12. Additionally, the cartridge 12 may include a receiving port 24 to interface with the vial 18 and / or cap 20 in order to receive the sample inside the cartridge 12.Figure 1E includes a high-level process flow illustrating the sample (e.g., saliva, mucus, nasal swab, oral swab, etc.) being introduced into cartridge 12 (through vial 18) and then cartridge 12 being inserted into reader 14.

[00189] The reader 14 automatically provides fluidic control, thermal control, and optical measurement of cartridge 12 within a test time of 15 to 45 minutes. In some embodiments, a reader 14 can accept various types of cartridges 12, including an expanded menu after distribution to the end user, allowing the end user to program the reader as needed. In some embodiments, a reader 14 will automatically detect the type of cartridge 12 and execute one or more indicated test sequences for one or more assays contained therein.

[00190] Figure 2A illustrates a positive reader outcome indicator, according to aspects of the present modalities. Figure 2B illustrates a negative reader outcome indicator, according to aspects of the present modalities. In some modalities, the re Petition 870250102472, dated 10 / 11 / 2025, p. 47 / 197 42 / 97 results are displayed by one or more indicators 26 (i.e., lit LEDs) on reader 14. In some modes, the results are displayed by means of combined indicators of lit LEDs on reader 14 and corresponding labels 28 (e.g., corresponding to diagnoses such as COVID-19, influenza, RSV, negative diagnoses, etc.) on cartridge 12 (see Figures 2A and 2B).

[00191] In some embodiments, a reader is a durable device that performs test processes in conjunction with consumable elements comprising a cartridge and / or sample collection.

[00192] In some embodiments, a reader is run in a vertical position. In some embodiments, a vertical position allows gravity-driven fluid movement (see Figure 1C) (i.e., fluids can gravity feed into the cartridge). In some embodiments, a reader is lightweight. In some embodiments, a reader is portable. In some embodiments, a reader can be powered by a standard USB wall charger, AC adapter, internal battery, disposable battery, and / or rechargeable battery.

[00193] Figure 3 illustrates a combined summary of the user workflow and the assay workflow 40, according to aspects of the present embodiments. Workflow 40 illustrates the time associated with each step of the process, as well as simultaneous user actions and chemical processes. For example, in step 32, workflow 40 may include sample collection 32 for a period of about 1 minute or less during which the user automatically collects a biological sample (e.g., from inside one or both nostrils), saliva or mucus, or other biological sample using the swab 16 (shown in Figure 1A), as illustrated in Figure 4A. The swab 16 is then agitated in the sample collector (or vial) 18 containing buffer, as shown in Figure 4B. During this time, the sample is chemically transferred to the buffer. Petition 870250102472, dated 10 / 11 / 2025, page 48 / 197 43 / 97 In some embodiments, the buffer may include a Tris buffer, for example, HCl buffer with a pH of about 8.8, or from about 8.6 to about 9.0. In step 34, the workflow 40 may include inserting the sample collector (or vial) 18 into the cartridge 12 for a period of about one minute or less, as shown in Figures 1D, 1E, and 5. In the embodiment of Figures 1D and 1E, a cap 20 is placed on the vial 18, and then the vial is turned upside down and inserted into the cartridge 12. In the embodiments of Figure 5, a suction device 48 (such as a syringe or dropper) may be used to transfer the sample from the sample collector (or vial) 18 to a reservoir 52 disposed on top of the cartridge 12. The cap 20 may then be secured on top of the reservoir 52.During this step (34) of the workflow 40, the user installs the cartridge 12 in the slot or cube 22 of the reader 14 and also installs the sample collector (or bottle) 18 in the cartridge 12 as shown in Figures 1E and 6, or alternatively transfers the sample to the cartridge as shown in Figure 5 and as explained above.

[00194] With further reference to Figure 3, workflow 40 may include thermal lysis in step 36, which, in some embodiments, may occur for a period of about 3 to about 5 minutes, during which cell lysis is performed. Thermal lysis is further described herein in conjunction with Figures 8A and 8B. In step 38, workflow 40 may include fluid transfer for a period of about 1 minute or less. Fluid transfer is further described in this document in conjunction with Figure 9. In step 42, workflow 40 may include carrying out a reaction for a period of about 10 to about 30 minutes. During this time, workflow 40 may include hydration of lyophilized beads, followed by amplification, Cas-12 activation and / or reporter cleavage. In step 44, workflow 40 may include providing a reading of the re Petition 870250102472, dated 10 / 11 / 2025, page 49 / 197 44 / 97 test results for a period of about 1 minute or less. During this time, the user views the diagnostic reading from the base station / reader 14 and the cartridge, as shown in Figures 2A, 2B and 7. The mode / system 10 of Figure 7 may include an alternative configuration in which the cartridge 12 is inserted horizontally (i.e., instead of vertically) into the reader 14. The mode / system 10 of Figure 7 may also include a panel 142 on the surface of the reader 14 that includes status LEDs. In step 46, the workflow may include disposing of the used cartridge 12 and the sample collector (or bottle) 18 in a conventional household waste receptacle (i.e., special disposal of the cartridge 12 and sample collector (or bottle) 18 is not required). Mechanical Subsystem

[00195] Figures 13 and 14 illustrate a reader clamping mechanism in an open and a closed position, respectively, according to aspects of the present embodiments. In some embodiments, the reader 14 comprises an internal mechanical subsystem or assembly 50. In some embodiments, a mechanical subsystem comprises an internal mechanical assembly and a clamping cover 54. An exemplary mechanical subsystem or assembly 50 is illustrated in Figures 13 and 14, which show internal components of the reader 14. The front outer casing of the reader 14 is not shown in Figures 13 and 14 so that the components of the mechanical subassembly 50 are visible. In the embodiments of Figures 13 and 14, the cover or clamp 54, when closed, pulls a linkage 56 upwards, thereby rotating a cam 58 around its axis (or first coupling) 62.Follower 88 is pushed away from cam 58 by the rotational movement of cam 58, in turn pushing cartridge 12 (to the right in the side view images of Figures 13 and 14) through the support plate 70. Consequently, when cover 54 is closed. Petition 870250102472, dated 10 / 11 / 2025, page 50 / 197 45 / 97 of, it ensures that cartridge 12 is fixed in the correct position within reader 14. Cam 58 can rotate around a first coupling 62. Cam 58 may include a fan-shaped portion 76 at one end which includes a curved edge and a curved groove 64 disposed therein. The curved groove 64 has increasing or decreasing depth so that when it interfaces with the follower 88 (see side views in Figures 13 and 14), the support plate is translated towards and / or away from cartridge 12 depending on whether the clamping cover 54 is being closed or opened. At an opposite end of the curved groove 64, the cam is rotatably coupled to the linkage 56 via a second coupling 64.The linkage may include a first linear element 72 and a second linear element 74 that are rigidly coupled and / or monolithic to each other and, in some embodiments, may be oriented so as to create an angle between them, the angle varying from about 125 to 180 degrees, or from about 135 to 175 degrees, or from about 140 to about 170 degrees, or from about 145 to about 165 degrees, or from about 150 to 160 degrees and / or other subranges between them. In some embodiments, the cam 58 may include a curved slot 92 to help support and hold the cam 58 correctly positioned as the cam 58 rotates around the first coupling 62. A tongue or protrusion (not shown) extending from the support wall 70 may extend through the curved slot 92, allowing the cam 58 to rotate around it when the cover 54 is being opened or closed.Support wall 70 is part of an internal device (i.e., inside the reader) to help facilitate the lateral movement of the cartridge within the reader. Cam 58 helps convert the closing (i.e., rotational) movement of the reader cover into the lateral movement of the internal device.

[00196] With reference again to Figures 13 and 14, at an extreme Petition 870250102472, dated 10 / 11 / 2025, page 51 / 197 46 / 97 opposite the coupling with the cam 58, the linkage 56 can be rotatably coupled to the cap 54 via a third coupling 66 disposed within the cap 54. When the cap 54 is opened and closed, the cap 54 rotates around a fourth coupling 68 which couples the cap 54 to the body of the reader 14 and, in turn, the linkage 56 and the cam 58 are actuated via the third and second couplings 66, 64, respectively. The assembly 50 may include a positioning system or sensor 60 located adjacent to and / or in the vicinity of the cap 20 and the vial 18 when they are inserted into the reader 14. The positioning system 60 detects when the cartridge 12 is correctly inserted and positioned within the reader 14, so that the assay workflow can begin and / or continue, as described in this document in conjunction with Figures 2225.The support plate 70 may include one or more support tabs 82 on each side to help facilitate the movement of the support plate 70 within the reader 14. The support tabs 82 may be rigidly coupled to the support plate 70 and may be configured with one or more through holes arranged therein so that they may slide in one or more horizontally oriented guides 68. In an open position, as shown in Figure 13, a horizontal gap 86 between the support tab 82 and the edge of the outer wall 78 is shown in the side view illustration. In comparison, in the side view illustration of Figure 14, the gap is not visible because the support plate 70 has translated to the right (toward the outer wall 78) in the closed position. In some embodiments, the assembly 50 may include one or more springs 84 arranged around the horizontal guides 68. As the cover 54 is closed, the springs 84 are compressed.When the cover 54 is opened, the springs 84 expand, thus pushing the support plate away from the outer wall (i.e., back wall) 78 of the reader 14. Petition 870250102472, dated 10 / 11 / 2025, page 52 / 197 47 / 97 Heating and Thermal Control

[00197] Figure 13 illustrates a reader clamping mechanism in an open position, in perspective view (left) and side view (right), according to aspects of the present embodiments. Figure 14 illustrates a reader clamping mechanism in a closed position, in perspective view (left) and side view (right), according to aspects of the present embodiments. In some embodiments, a cartridge 12 is installed in a reader 14 by insertion into a vertical slot 22 when a clamp (i.e., cover 54) is in an open position (Figure 13). In some embodiments, when a clamp / cover 54 is closed to a position (Figure 14) where it locks closed (closed position). In some embodiments, a clamp closing action actuates a mechanical linkage 56 that accurately translates and locates the cartridge 12 to the optical module.

[00198] In some embodiments, a reader 14 comprises a reader thermal subsystem. In some embodiments, a reader thermal subsystem 90 heats the cartridge lysis chamber 94 and maintains precise control using an open-loop strategy (Figures 8A and 20).

[00199] In some embodiments, a reader thermal subsystem 90 heats a cartridge reaction chamber 94 and maintains precise control using an open-loop strategy (Figure 20A). This eliminates the need for sensors in the cartridge. For example, as shown in Figure 8B, the lysis heating element 116 includes a temperature sensor 120 that is used in a feedback circuit that maintains the heater temperature at approximately 100 degrees C (by repeated activation and deactivation of the heater, as illustrated by the lysis temperature 110 in Figure 20A). The heat is then transferred through a heat spreader 118 (e.g., Petition 870250102472, dated 10 / 11 / 2025, p. 53 / 197 48 / 97 a first heat spreader 118 (see Figure 8B) positioned between the heating element 116 and the lysis chamber 94 so that the temperature at the bottom 112 and top 114 of the lysis chamber 94 is maintained at a temperature around 90 degrees C (+ / - 1-2 degrees C), as shown in Figure 20A. Therefore, provided that the temperature 110 in the lysis heating element 116 is maintained at or around 100 degrees C, the temperature in the lysis chamber will be maintained at the target temperature of about 90 degrees C. Therefore, temperature sensors are not required in the lysis chamber itself. Each of the first and second heating elements 116, 126 may be or include resistance heaters and / or film heaters. In some embodiments, each of the first and second heating elements 116, 126 are located on opposite sides of cartridge 12 of PCBA 150.In some versions, each of the first and second heating elements 116, 126 are integrated directly into PCBA 150.

[00200] Referring again to Figure 8A, the lysis chamber 94 may include a lower conical portion 96 that helps to narrow the biological solution out of the lysis chamber 94 when a ball valve 98 is activated after the completion of the lysis heating. The biological solution may then flow through a vertical passage 104 and eventually into a plurality of reaction chambers 106, each comprising at least one lyophilized sphere and each fluidly coupled to a vent hole 109 covered by a vent membrane 108, both located in the cartridge 12 vertically above the respective reaction chamber 106 to which it is coupled. In some configurations, the 12-gauge cartridge may have a height of approximately 70 mm to approximately 120 mm, or approximately 75 mm to approximately 115 mm, or approximately 80 mm to approximately 110 mm, or approximately 85 mm to approximately 105 mm, or approximately 90 mm to approximately Petition 870250102472, dated 10 / 11 / 2025, p. 54 / 197 49 / 97 of 100 mm, or approximately 95 mm. In some embodiments, the cartridge 12 may include a width of approximately 40 mm to approximately 90 mm, or approximately 45 mm to approximately 85 mm, or approximately 50 mm to approximately 80 mm, or approximately 55 mm to approximately 75 mm, or approximately 60 mm to approximately 70 mm, or approximately 75 mm. The thermal reading subsystem 90 may also include one or more mechanical supports 130 to which the heat spreader 118 (e.g., a first heat spreader 118) and / or the heating element 118 may be mounted.

[00201] Figure 9 illustrates the transfer of a biological solution to reaction chambers 106, according to aspects of the present embodiments. In the embodiment of Figure 9, gravity pulls the solution through an internal passage to the 8 reaction chambers shown. A total fluid volume can be on the order of 500 microliters, which provides sufficient hydrostatic head to overcome capillary action and drive the fluid to the reaction chambers. After the biological solution exits the lysis chamber 94 through the vertical passage 104, it flows to the first and second horizontal passages 132, 134, each fluidly coupled to a plurality (e.g., 2, 3, 4, 5, 6) of reaction chambers 106.The hydrostatic pressure created by the biological solution or fluid in the vertical passage 104 is sufficient to push any residual gas in the passages out through the vent membranes 108 and vent holes 109, although it is also sufficient to push the biological fluid into each of the reaction chambers 106, through the first and second horizontal passages 132, 134. In some embodiments, the vent membranes 108 include hydrophobic openings that allow each of the reaction chambers 106 to fill (i.e., allowing gases to escape from the passages as they are filled with liquids). Each of the passages 104, 132, 134 is di. Petition 870250102472, dated 10 / 11 / 2025, p. 55 / 197 50 / 97 mentioned so that the total fluid contained is of a volume large enough to create a hydrostatic head and so that the internal diameters are not so small as to create excessive resistance to flow or surface tension, while also being small enough to prevent the formation of air bubbles. For example, in some embodiments, the internal diameters of channels or passages 104, 132, 134 are in a range of about 400 μm to about 1200 μm, or about 500 μm to about 1100 μm, or about 600 μm to about 1000 μm, or about 700 μm to about 900 μm, or about 750 μm to about 850 μm, or about 800 μm. In some embodiments, the volume of each reaction chamber 106 is from about 30 μL to about 50 μL or from about 35 μL to about 45 μL, or about 40 μL. In some embodiments, the cartridge 12 includes about 5, 6, 7, 8, 9 or 10 reaction chambers 106.In some embodiments, the total volume of passages or channels 104, 132, 134 (i.e., dead volume) is from about 50 μL to about 150 μL. Consequently, the total volume of fluid required to fill the cartridge may vary from about 200 μL to about 650 μL, or from about 300 μL to about 550 μL, or from about 400 μL to about 500 μL and / or other subranges in between.

[00202] Figure 10A illustrates the heating of the reaction chamber in cross-sectional view, according to aspects of the present embodiments. With reference to Figure 10A, cartridge 12 may include a heating zone of the reaction chamber 136, according to aspects of the present embodiments. While the biological fluid is flowing from the lysis chamber to the reaction chambers, as described in this document, the biological fluid is passively cooled from a temperature of about 90 degrees C to about 60 degrees C. The heating element of the reaction area 126 (i.e., a second heating element, the heating element of the lysis area 116) Petition 870250102472, dated 10 / 11 / 2025, p. 56 / 197 51 / 97 (being the first heating element) reaches and maintains a temperature of about 63 degrees C, thus producing reaction chamber temperatures in a range of about 59 degrees C to about 60.5 degrees C, or about 60 degrees C, as shown in Figure 20B, left side. Figure 20B, right side, shows the temperature of the lysis heater 110 and the temperature of the reaction heater 126, both plotted as a function of time. The lysis heater first heats up to a temperature of about 100 degrees C, as described in this document. After lysis, the lysis heater cools passively and the reaction heater heats up to a temperature of about 63 degrees C. Figure 10B illustrates a side view of the heating zone of the reaction heater, according to aspects of the present embodiments.As shown in Figure 21, each of the temperatures of the eight reaction chambers 106 is maintained at a temperature within a range of about 59.0 degrees C to about 62.5 degrees C with an average temperature of reaction chamber 106 being about 61.25 degrees C. These reaction chamber 106 temperatures (i.e., in the range of 59 to 62.5 degrees C) are achieved by maintaining the heater / heating element of reaction chamber 126 at a temperature range of about 63-64 degrees C (again, in an open-circuit configuration with the reaction chambers 106 themselves).

[00203] In some embodiments, the reaction temperatures are uniform and repeatable in all cartridge chambers (e.g., eight chambers) (Figure 20B, left side and Figure 21).

[00204] In some embodiments, a reader 14 comprises a heater (for example, a lysis heater or heating element 116 and a second heater which includes a reaction area heater or heating element 126). In some embodiments, a reader 14 comprises a film heater. In al Petition 870250102472, dated 10 / 11 / 2025, page 57 / 197 52 / 97 In some embodiments, a reader 14 can heat an area of ​​a cartridge. In some embodiments, a reader comprises a film heater for heating an area of ​​a cartridge. In some embodiments, a reader is capable of heating a cartridge lysis chamber, as described in this document, to about 80 °C to about 100 °C, such as about 85 °C to about 95 °C. In some embodiments, a contact pressure between a heating element 116, 126, a heat spreader 118, 128 and / or an area to be heated 94, 106 is provided by the mechanical clamping mechanism after installation (see Figures 13 and 14). In some embodiments, the heat spreaders are composed of aluminum and / or other conductive materials and comprise a thickness of about 0.08 inch to about 0.2 inch.

[00205] In some embodiments, a reader 14 is capable of heating a cartridge reaction chamber area 106 to about 50 °C to about 70 °C, such as about 60 °C (or about 58 °C to about 63 °C, or about 58 °C to about 62 °C, or about 59 °C to about 62 °C, or about 59 °C to about 61 °C, and / or other subranges between about 57 °C and about 64 °C) during the duration of a reaction (for example, during the duration of an amplification, or during the duration of another reaction). In some embodiments, a reaction chamber area of ​​cartridge 106 of a cartridge 14 is heated to a target temperature of about 60 °C by a compliant heating plate or heat spreader 128 in a reader 14. In some embodiments, a contact pressure is provided by the mechanical clamping mechanism after installation, as described in this document. Optical Module

[00206] Figure 15A illustrates an optical module 140 including an optical printed circuit board (PCBA) assembly according to Petition 870250102472, dated 10 / 11 / 2025, p. 58 / 197 53 / 97 aspects of the present embodiments. Figure 1B illustrates the same embodiment as Figure 15A with an overlapping cartridge, according to aspects of the present embodiments. In some embodiments, a reader 14 comprises an optical module 140. An optical module 140 can measure fluorescence. When a cartridge 12 is inserted, the optical module 140 is not yet required in the operating sequence (Figure 23A and B and Figure 24A). In some embodiments, an optical module 140 comprises one or more photodetectors. The photodetectors of the optical module can be used for other tasks, such as identifying the cartridge 12 when it is inserted into the reader 14, as discussed in more detail below.

[00207] In some embodiments, an optical module is tuned to a specific dye (e.g., a specific excitation and / or emission). In some embodiments, an optical module is tuned to the FAM dye (excitation at 460 nm, emission at approximately 540 nm or in some embodiments with an absorption / excitation wavelength of 495 nm and an emission wavelength of about 517 nm and / or in some embodiments with an absorption / excitation wavelength in a range of about 450 nm and an emission wavelength in a range of about 500 nm to about 550 nm). In some embodiments, the FAM dye comprises a carboxyfluorescein molecule that includes a carboxyl group.

[00208] In some embodiments, an optical module 140 comprises a filter. In some embodiments, a filter is a gel filter 160 (shown in Figures 19A and 19B). In some embodiments, a filter is a 520 nm long-pass filter. In some embodiments, the gel filter is composed of and / or comprises polyester and / or cellulose acetate and may be adhered to the photodetector 144, 162 by means of an optical adhesive. The gel filter may include a thickness of about Petition 870250102472, dated 10 / 11 / 2025, p. 59 / 197 54 / 97 0.004 inches to about 0.008 inches (i.e., 4-8 mils).

[00209] During cartridge 12 insertion, if an add-on LED excitation wavelength that is beyond the 520 nm long-pass filter is used, photodetectors can be used to measure cartridge label ID intensity reflections. It is these reflections that can be uniquely printed in a variety of patterns to provide an identification characteristic (ID) (also referred to in this document as a barcode) on a label.

[00210] In some embodiments, a label may be as small as 2, 4, 6, 8, 10 and / or other unique ID numbers or as many as 256 or more. Label reading operation with optical module 140 may be via a static mode (when inserted) or dynamic mode (during insertion). Label color and printing materials may vary from simple white label with black ink to fluorescent marking ink and other color combinations. The label may be affixed to cartridge 12 via adhesive, or the optical targets may be printed directly or injection molded into the cartridge plastic.

[00211] In some embodiments, an optical module 140 uses simple and low-cost components. The optical components align with the cartridge reaction chambers after installation (see Figure 15B). For example, as shown in Figure 15A, the optical module 140 may include a first row 148 of optical components and a second row 152 of optical components. For example, each of the first and second rows 148, 152 may include four photodetectors (e.g., 4 photodiodes 144) and 4 LEDs 146, for a total of 8 photodiodes 144 and 8 LEDs 146. Each of the 8 LEDs 146 may be spaced relative to each other to coincide with the spacing of the reaction chambers 106 shown in Figures 8A, 9, Petition 870250102472, dated 10 / 11 / 2025, p. 60 / 197 55 / 97 10A and 27, so that LEDs 146 can be used to illuminate and excite reaction chambers 106. The excitation light from an LED in the PCBA strikes a corresponding reaction chamber, and the fluorescence from a sample in the reaction chamber travels to the photodetector 144. As shown in Figures 13 and 14, the PCBA (i.e., printed circuit board) 150 is visible through the support wall 70 inside the reader 14. In Figure 15B, the cartridge 12 is shown superimposed on the PCBA 150, illustrating the reaction chambers 106 of the cartridge 12 aligned with the LEDs 146 and photodetectors 144 of the optical module 140. In the view shown in Figure 15B, the heat spreaders 118, 128 and the heating elements 116, 126 would be placed in front of the cartridge 12 (i.e., protruding from the page).In other words, once cartridge 12 is installed in reader 14 and positioned as described in Figures 13 and 14 above, cartridge 12 is sandwiched between heat spreaders 118, 128 and PCBA 150. Consequently, when cartridge 12 is installed in reader 14, the PCBA assembly will be adjacent to cartridge 12 on a first side, so that LEDs 146 can excite reaction chambers 106 and photodetectors 144 can detect the fluorescence emitted from it, while at the same time, heat spreaders 118, 128 and heating elements 116, 126 will be adjacent to cartridge 12 on a second side of the cartridge (the second side of the cartridge being opposite the first side of the cartridge), so that heat spreaders 118, 128 and heating elements 116, 126 can heat both the lysis chamber 94 and the reaction chambers 106.

[00212] In some embodiments, during the amplification reaction, the reaction chambers 106 of cartridge 12 are excited by blue LEDs 156 (centered at about 465 nm wavelength, or for example, in a range of about 430 nm to about Petition 870250102472, dated 10 / 11 / 2025, p. 61 / 197 56 / 97 490 nm) as shown in Figure 16.

[00213] Figure 17 illustrates emission and excitation spectra of fluorescein, according to aspects of the present embodiments. In some embodiments, a positive reaction (amplification) in a reaction chamber 106 produces a logistic type increase in the fluorescent response to excitation using a fluorescent dye (i.e., Fluorescein) (Figure 17). For example, as shown in Figure 17, an excitation spectrum 154 can range from about 440 nm to about 520 nm and can be centered at about 490 nm, while an emission spectrum 156 can range from about 480 nm to about 560 nm and can be centered at about 515 nm.

[00214] Figure 18 illustrates a transmission spectrum for a Kodak Wratten 2-12 optical filter, according to aspects of the present embodiments. In some embodiments, a reflective fluorescent emission from the reaction chambers is filtered through a 160 low-pass filter (i.e., Kodak Wratten 2-12 gel filter) (Figure 18). As shown in Figure 18, the transmission is only about 1% at wavelengths of 500 nm and below, about 12% at a wavelength of 510 nm, about 46% at 520 nm, about 74% at 530 nm, about 85% at 540 nm, and more than 90% (e.g., about 95%) at wavelengths of 550 nm and above. Therefore, according to aspects of the present embodiments, the low-pass filter can be configured so that substantially all the light in the excitation spectrum 154 is filtered out, while substantially all the light in the emission spectrum 156 is able to be detected. The filter 160 is shown in Figures 19A and 19B.

[00215] Figure 19A illustrates an optical PCBA with photodiodes, according to aspects of the present embodiments. Figure 19B illustrates an optical PCBA with phototransistors, according to aspects of the present embodiments. In some embodiments, two architectures Petition 870250102472, dated 10 / 11 / 2025, p. 62 / 197 57 / 97 optical configurations were successfully implemented – one using photodiodes and one using phototransistors (Figure 19A and B). In some embodiments, the red LEDs 158 are used for cartridge identification. For example, as shown in Figure 19A, in some embodiments, PCBA 150 may include photodiodes 144, the first set of LEDs 146 (i.e., blue LEDs), and a second set of LEDs 158 (i.e., red LEDs). In some embodiments, the blue LEDs 146 are used for excitation of the reaction chambers 106, while the red LEDs 158 are used to identify the cartridge 12, as further described below. In some embodiments, the red LEDs 158 are positioned adjacent to the photodetectors 144, 162 at approximately 90 degrees from the position of the blue LEDs 146 in relation to the photodetectors 144, 162. In other words, the red and blue LEDs 158, 146 can be spaced approximately 90 degrees apart in relation to the photodetectors 144, 162.The PCBA 150 may also include filter 160 (i.e., low-pass filter 160) and optical shielding 336. In some embodiments, the positions of the blue LEDs 146 and the red LEDs 158 are reversed (and the positions of other features, such as marker identification, may also be adjusted to match the positions of the red LEDs 158, for example). In the embodiment of Figure 19B, the PCBA 150 includes a phototransistor 162 in place of the photodiode 144 in Figure 19A. Therefore, PCBA 150 may include a plurality of photodetectors that include photodiodes 144 and / or phototransistors 162. In some embodiments, a lateral spacing (center to center) between each of the blue and red LEDs 146, 158 and the photodetectors 144, 162 may be from about 3 mm to about 9 mm, or from about 4 mm to about 8 mm, or from about 5 mm to about 7 mm, or about 5 mm, or about 6 mm, or from about 5 mm to about 6 mm. Software / Firmware Petition 870250102472, dated 10 / 11 / 2025, page 63 / 197 58 / 97

[00216] In some embodiments, a reader comprises software and / or firmware. The system's software requirements are defined as a subsystem in an SRS (Software Requirements Specification). General Sequence Control

[00217] In some embodiments, a basic operating sequence 170 of a test run is shown in Figure 22. The general timing and sequence of a test run are shown in Figure 23A and the timing and sequence of the cartridge ID function are shown in Figure 23B. The timing and sequence of the cartridge ID function are shown in Figure 24A and the timing and sequence of the fill detection function are shown in Figure 24B. The timing and sequence of the optical fluorescence measurement during amplification are shown in Figure 25A and the detailed timing and sequence of the optical fluorescence measurement are shown in Figure 25B.

[00218] With reference to Figure 22, which illustrates an exemplary operating flow according to the present embodiments, the basic operating sequence or method 170 may include the following steps: applying power 166 in the initial step, performing a system initialization sequence in step 168, and confirming the reader's ready state in step 172. The basic operating sequence or method 170 may include the following additional steps: In step 188, preparing cartridge 12 (by the user) with a sample; in step 174, inserting cartridge 12 into reader 14; in step 176, detecting cartridge identification; in step 178, pressing the reader and executing the automatic start-up routine; in step 180, performing a test run; in step 182, performing the test or trial and displaying the results; in step 184, removing cartridge 12 from reader 14 and discarding cartridge 12; and in step 186, turn off reader 14 (that is, turn off reader 14). Petition 870250102472, dated 10 / 11 / 2025, page 64 / 197 59 / 97

[00219] In some modes, when configured for disconnected use, the system (i.e., reader 14) reports the test result to the user visually (e.g., each test lights up for a positive result, as shown in Figure 2A). In some modes, reader 14 does not save detailed test data or transmit it to any other system or device.

[00220] In some modes, when configured for connected use, reader 14 can transmit data via Bluetooth wireless radio. This data may include: test programs and parameters, firmware and software updates, user-entered information from mobile phone applications, test results, raw test data, error codes, and test execution metadata.

[00221] In some embodiments, a reader 14 may include an alternative form to, for example, optimize usability and workflow. Feasible industrial design concepts 700 for the systems are shown in Figure 41. For example, industrial design concepts may include a cartridge 702 configured to be inserted horizontally into a corresponding reader 704, as well as a reader 706 with a top surface that is at least partially angled and at least partially flat (i.e., at least partially parallel to a horizontal plane).

[00222] Alternative user workflows 800 are shown in Figures 42A, 42B and 42C. A first alternative workflow 810 is shown as Concept A in Figure 42A and may include the following steps: In step 802, place the cartridge in the cube; in step 804, remove the foil covering the container containing the buffer; in step 806, mix the swab in the container; in step 808, push a cap onto the tube; in step 812, twist the tube onto the cartridge and proceed with the test according to the present description.

[00223] With reference to Figure 42B, a second workflow Petition 870250102472, dated 10 / 11 / 2025, page 65 / 197 Alternative 60 / 97 830 is shown as Concept B and may include the following steps: In step 814, remove the top sheet and place the tube in a cap on the holder (i.e., the reader); in step 816, mix the swab in the container; in step 818, close the tube cap; in step 820, secure the cartridge in the upright position; in step 822, secure the tube to the cartridge; in step 824, insert the tube with the cartridge into the reader. In step 826, the second alternative workflow 830 may include puncturing the tube (i.e., through the cap) to encourage fluid flow. In step 828, the second alternative workflow 830 may include proceeding with the test according to this disclosure.

[00224] With reference to Figure 42C, a third alternative workflow 840 is shown as Concept C and may include the following steps: In step 832, insert the tube into the cartridge without piercing the bottom of the tube; in step 834, remove the tube foil; in step 836, mix the swab in the container; in step 838, push the plunger cap into the tube, thus forcing the fluid into the lysis chamber. In some embodiments, this may include the use of measuring features. The third alternative workflow 840 may further include the following steps: In step 842, insert the cartridge and tube into the reader; and in step 844, proceed with the test after insertion into the reader is complete. In some embodiments, the system 100 may include a pierceable foil.

[00225] Figure 23A shows a general timing sequence 200 for the operation of cartridge 12, reader 14 and the system 10 in general (i.e., the timing sequence for a complete system run). For example, the general timing sequence 200 includes timings for LED status indicator 188, timing sequence for cartridge insertion 190, cartridge identification 192, cartridge fixation 194, lysis heating 196, valve actuation 198, fill detection 202, heating of Petition 870250102472, dated 10 / 11 / 2025, page 66 / 197 61 / 97 LAMP 204 and results display 206, among other timings. The overall sequence time 200 also includes a time bar 208 (Figure 23A) illustrating the time corresponding to each step in the sequence. For example, cartridge insertion 190 begins at approximately 1 minute and 25 seconds and the cartridge remains inserted for approximately 33 minutes until about 5 or 10 seconds before the end of the overall sequence. In another example, valve actuation 198 occurs during a period of approximately 10 seconds after lysis heating 196.

[00226] Figure 23B illustrates the timing sequence 210 associated with the cartridge identification process or algorithm 1700. The cartridge identification process or algorithm 1700, at a high level, is illustrated in Figure 38. The 1700 process may include the following steps: In step 1702, system initialization; in step 1704, system idle time; in step 1706, cartridge insertion and identification detection; in step 1708, performing one or more optical checks; in step 1710, executing the identification routine; and in step 1712, concluding with the sending of an internal communication to the microprocessor (inside the reader) confirming the cartridge identification.As illustrated in Figure 23B, the cartridge identification sequence time 210 may include LED status indicator times 188, cartridge fixation 194, cartridge position detection 216 (i.e., detection of whether cartridge 12 is fully inserted), activation of red LEDs 212, activation of blue LEDs 218, and photodetector readings 214 from each of the eight (8) photodetectors (channels 18). As illustrated, the cartridge identification sequence time 210 may include cycling through each of the 8 photodetector channels sequentially and then repeating the cycles multiple times (e.g., 3, 4, 5, 6, 7, 8, 9 and / or more than 9 times) to read the identification markings on cartridge 12, as described in this document. Petition 870250102472, dated 10 / 11 / 2025, p. 67 / 197 62 / 97 document.

[00227] Figure 24A illustrates a cartridge identification sequence timing 220 in a high-speed mode, according to aspects of the present embodiments. At a high level, the high-speed mode cartridge identification sequence timing 220 follows the same process flow shown in Figure 38 as the normal mode. The high-speed mode cartridge identification sequence timing 220 is similar to the sequence timing 210 shown in Figure 23B, except that it includes a first sequential activation period 222 of the first four (4) photodetector channels at the higher frequency followed by a second sequential activation period 224 of all eight (8) photodetector channels at the normal frequency, with the normal frequency being approximately half the higher frequency.

[00228] Figure 24B illustrates a timing sequence of fill detection algorithm 230, according to aspects of the present embodiments. The fill detection algorithm 1800 or process, at a high level, is illustrated in Figure 39. The fill detection algorithm or process 1800 may include the following steps: In step 1802, lysis (e.g., by means of lysis heating in the lysis chamber 94); in step 1804, a delay after the period during which lysis is occurring and, in some embodiments, concomitant with or before the activation of the ball valve. As described in this document, after the activation of the ball valve, the biological solution flows from the lysis chamber 94 to the reaction chambers 106 (during which the biological solution is passively cooled).The 1800 process may also include the following steps: In step 1806, perform the fill detection algorithm; in step 1808, perform loop-mediated isothermal amplification (LAMP); and in step 1810, complete the fill detection routine. Petition 870250102472, dated 10 / 11 / 2025, page 68 / 197 63 / 97 ment and communication, by the microprocessor, that the cartridge filling detection routine is complete (and filling was detected or not detected). As shown in Figure 24B, in some embodiments, the filling detector 226 is initiated simultaneously with the activation (or actuation) of the ball valve and occurs at a frequency of 10 Hz (or from about 5 Hz to about 20 Hz, or from about 3 Hz to about 50 Hz, or from about 2 Hz to about 100 Hz and / or other sub-ranges between them). In some embodiments, the actuation of the ball valve 98 occurs through mechanical means. In some embodiments, system 10 includes thermal means (e.g., the heating element of the lysis area 116) to actuate the ball valve 98. In some embodiments, simultaneously with the start of the fill detector 226, the sequence time of the fill detection algorithm 230 may include monitoring of singles 228 for fill activity.

[00229] Figure 25A illustrates a timing sequence for measuring LAMP 240 fluorescence, according to aspects of the present embodiments. The timing sequence for measuring LAMP 1900 fluorescence, or process, at a high level, is illustrated in Figure 40. Process 1900 may include the following steps: In step 1902, perform (or complete) the fill detection routine; in step 1904, acquire LAMP fluorescence (i.e., through the photodetectors and LEDs as described in this document); in step 1902, display a result after acquiring LAMP fluorescence; in step 1908, completion of the LAMP fluorescence acquisition routine and communication, by / to / within the microprocessor, that the LAMP fluorescence acquisition routine is complete. As shown in Figure 25A (and Figure 24B), in some embodiments, the heating of the LAMP 232 reaction is initiated simultaneously with the completion of the filling detector 226.The sequence Petition 870250102472, dated 10 / 11 / 2025, page 69 / 197. The timing sequence 240 may also include the LAMP fluorescence acquisition mode 234 being initiated slightly after (e.g., 1, 2, 5, 10, 20, or 30 seconds after) the heating of the initiation LAMP reaction 332. The timing sequence 240 may also include the initiation of the signal curve algorithm monitoring 236 simultaneously with the initiation of the LAMP fluorescence acquisition mode 234. Finally, as shown in Figure 25A, the timing sequence 240 may also include the initiation of the call algorithm 238 after (i.e., simultaneously with) the completion of each of the LAMP reaction heating 232, LAMP fluorescence acquisition mode 234, and signal curve algorithm monitoring 236.

[00230] Figure 25B illustrates an A / D timing sequence for fluorescence measurement of LAMP 250, according to aspects of the present embodiments. The A / D timing sequence for fluorescence measurement of LAMP 250 allows oversampling, thus increasing the resolution of fluorescence acquisition. The LAMP 250 fluorescence measurement A / D timing sequence in Figure 25B is illustrated in terms of a single channel (i.e., for only a single reaction chamber 106 (CH1), as well as corresponding LEDs and photodetectors), but would also apply with equal force to any and all reaction chambers / channels 106. The LAMP 250 fluorescence measurement A / D timing sequence may include initiating the LAMP 242 fluorescence acquisition mode (e.g., in 10-second scans) including acquisition in each of the reaction chambers 106 (e.g., channel 1 (CH1) acquisition 244).The LAMP 250 fluorescence measurement A / D timing sequence can also include the activation of 246 blue LEDs in synchronization (e.g., at a frequency of 100 ms) with the scans of reaction chamber 244. After an LED delay. Petition 870250102472, dated 10 / 11 / 2025, p. 70 / 197 65 / 97 of 20 ms 252, a reading of the photodetector CH1 248 is performed and the A / D oversampling acquisition of the photodetector 254 is initiated (e.g., at 10 ms intervals, repeated for several cycles, followed by a period (e.g., 30 ms to 50 ms of inactivation, followed by a second and subsequent activation periods at 10 ms intervals). During the second period of A / D oversampling acquisition of photodetector 254, a dark current reading 256 can be performed. The specific A / D acquisition 258 can also be initiated at 50 ms intervals after the LED delay 252. Finally, the LAMP 250 fluorescence measurement A / D timing sequence may include performing signal processing 262 (i.e., to help facilitate data storage) upon completion of each interval-specific A / D acquisition. 50 ms 258. B. Cartridge Assembly

[00231] In some embodiments, the present disclosure provides a cartridge 12. In some embodiments, a cartridge 12 is assay-specific (agnostic). In some embodiments, a cartridge 12 is a disposable cartridge. In some embodiments, a cartridge 12 is a low-cost disposable device comprising a plurality of reagents for detecting a target nucleic acid.

[00232] In some forms, a 12 cartridge interfaces with a 14 reader.

[00233] With reference to Figures 26 and 27, according to these embodiments, a cartridge set 260 may include cartridge 12, a plurality of ventilation membranes 108, a ball valve 98, a lyophilized lysis sphere 266, a plurality of lyophilized PCR spheres 268 and a front film 270. The lyophilized lysis sphere 266 may be preloaded into the lysis chamber 94 while each of the plurality of (e.g., eight (8)) lyophilized PCR spheres 268 may be preloaded into the respective plurality Petition 870250102472, dated 10 / 11 / 2025, p. 71 / 197 66 / 97 of (for example, eight (8)) reaction chambers 106. Consequently, when the cartridge assembly 260 is fully assembled, each of the lyophilized reaction / PCR beads 268 and the lysis bead 266 are arranged between the cartridge 12 and the film 270 so that they are partially encapsulated in the respective reaction chambers 106 or lysis chamber 94, with the film 270 holding them in place. In some embodiments, the lyophilized reaction / PCR beads 268 may include C7 FAM reporter, RS9 enzyme, DNA polymerase, dNTPs, buffer and corresponding primers and guides thereof. In some embodiments, due to the material properties of the film 270, the film 270 acts as a heat spreader 128, thus helping to allow heat transfer from the heating element of the reaction area 126 to the reaction chambers 106.As shown in Figure 27, the cartridge assembly 260 may include an additional vent membrane 272 (i.e., a ninth vent membrane 272 in addition to the eight (8) vent membranes 108 used to vent each of the eight (8) reaction chambers 106 during filling). The additional vent membrane 272 may be used in connection with the vent hole 274 to vent the lysis chamber 94 (i.e., allowing air to escape) when the cartridge 12 is initially filled through the lysis chamber 94. The cartridge assembly 260 may also include a valve film 264 to hold the ball valve 98 in place and to facilitate the actuation of the ball valve 98, which in some embodiments may include a diameter of 3 mm. In some embodiments, the cartridge 12 may be molded (e.g., by injection molding). In some applications, the 12-pound cartridge can be 3D printed or formed through machining, for example, through CNC drilling.In some embodiments, the 98 ball valve may be coated with a lubricant (e.g., a polymer coating). Petition 870250102472, dated 10 / 11 / 2025, p. 72 / 197 67 / 97 of parylene)) to facilitate the actuation of the ball valve 98 and to provide a moisture barrier to protect the ball valve 98 from corrosion or deterioration due to exposure to the biological solution (i.e., saliva and the buffer / reagent mixture). In some embodiments, the film 270 (i.e., front film 270) may include or be a microfluidic layer film with a thickness of about 0.003 inch to about 0.008 inch, for example, with a thickness of about 0.003, about 0.004, about 0.005, about 0.006, about 0.007, about 0.008 inch and various sub-strips in between. In some embodiments, the front film 270 may include a polypropylene laminate with an adhesive layer. In some embodiments, the front film 270 (i.e., film layer 270) may be thermally, laser and / or ultrasonically welded to the cartridge 12.

[00234] In some embodiments, a cartridge 12 comprises an injection-molded cartridge body 284. An exemplary cartridge body 284 is shown in Figures 6 and 29. In some embodiments, a cartridge body 284 is a plastic cartridge body. In some embodiments, a plastic cartridge body is made of a plastic polymer selected from the groups consisting of polycarbonate, polymethyl methacrylate (PMMA), cycloolefin polymer (COP), and cycloolefin copolymer (COC).

[00235] In some embodiments, one or more reaction chambers 106 are molded into the cartridge body 284. In some embodiments, 1 to 30 reaction chambers 106 (for example, 2 to 20, 4 to 16, 5 to 15, 6 to 12, 7 to 10 or about 8) are molded into the cartridge body 284. In some embodiments, the reaction chambers 106 are fluidly connected to a sample lysis chamber 94 via a valve (not shown). In some embodiments, multiple reaction chambers 106 are molded into the plastic body 284. A color Petition 870250102472, dated 10 / 11 / 2025, p. 73 / 197 The exemplary cartridge 68 / 97 284 comprising 8 reaction chambers 106 is represented in Figure 29; the number of reaction chambers may vary from 1 to 30.

[00236] In some embodiments, a cartridge 12 comprises one or more reaction chambers 106. In some embodiments, a cartridge comprises two or more reaction chambers 106. In some embodiments, a cartridge comprises three or more reaction chambers 106. In some embodiments, a cartridge comprises four or more reaction chambers 106. In some embodiments, a cartridge comprises five or more reaction chambers 106. In some embodiments, a cartridge comprises six or more reaction chambers 106. In some embodiments, a cartridge comprises seven or more reaction chambers 106. In some embodiments, a cartridge comprises eight or more reaction chambers 106.

[00237] In some embodiments, the volume of the reaction chamber 106 is from about 5 μL to about 100 μL (such as from about 10 μL to about 60 μL, such as from about 20 μL to about 50 μL, such as from about 40 μL). In some embodiments, a reaction chamber 106 comprises a lyophilized reagent. In some embodiments, a reaction chamber 106 is sealed by a film layer 270 (shown in Figure 27).

[00238] In some embodiments, one or more reaction chambers 106 comprise lyophilized reagents. In some embodiments, a detection system 10 comprises lyophilized spheres. In some embodiments, a lyophilized sphere 268 (shown in Figure 27) is used to verify the filling of each reaction chamber 106. A change in fluorescence that occurs when a lyophilized sphere 268 is rehydrated can be measured and used to verify the filling of the reaction chamber 106 with a sample.

[00239] In some forms, this disclosure provides Petition 870250102472, dated 10 / 11 / 2025, p. 74 / 197 69 / 97 a disposable cartridge 12 for detecting a target nucleic acid, the disposable cartridge 12 comprising a lysis chamber 94 (e.g., a first chamber or first heating zone) for receiving a sample comprising the target nucleic acid; a reaction chamber 106 connected via a first channel 104 (shown in Figure 9) to the lysis chamber and connected via a second channel 286 (e.g., a vent channel 286, shown in Figures 26 and 27) to a first vent hole 274.

[00240] Cartridge 12, in some embodiments, is a single-use element that receives the sample, contains the dry reagents, and performs the assay within a reader 14. Cartridge 12 is sealed by a cap 20 (shown in Figure 1) after sample transfer and contains all reagents and reaction products during and after the test. Cartridge 12 contains the dry reagents (in the form of lyophilized spheres 255, 268) within the reaction chambers and the lysis chamber (Figure 27).

[00241] With reference again to Figure 29, in some embodiments, a cartridge body 284 comprises a sample lysis chamber 94. In some embodiments, a cartridge body 284 comprises a sample entry port 288. In some embodiments, a cartridge body 284 comprises a label 290. In some embodiments, a cartridge body 284 comprises a unique device identification (UDI) barcode 292. In some embodiments, a cartridge body 284 comprises a result display 294. Venting membranes 108 are also illustrated in Figure 29, each being disposed in the cartridge body 284 and vertically spaced above each respective reaction chamber 106 to which it is fluidly coupled.

[00242] In some embodiments, a cartridge assembly 260 includes a fluid ball valve 98, hydrophobic openings 101, Petition 870250102472, dated 10 / 11 / 2025, page 75 / 197 70 / 97 272 and two cover films 264, 270 (Figure 27). In some embodiments, the cartridge body 284 is the primary component and is constructed mainly of an optically clear polymer (such as polycarbonate, COC, COP, etc.).

[00243] Alternatively, the 284 cartridge body may be constructed from optically clear material only in the reaction chamber areas 106 and other material (i.e., a non-optically clear material) elsewhere (such as using a 2-shot injection molding process, insert molding process or other assembly method).

[00244] In some embodiments, a cartridge 12 may be in an alternative form to, for example, optimize usability and workflow. Feasible industrial design concepts for the systems are shown in Figure 41. Alternative form factors for the cartridge 12, sample collection, and user workflow are shown in Figures 42A, 42B, and 42C.

[00245] In some embodiments, a cartridge 12 comprises a Cas enzyme, a probe and a guide.

[00246] In some embodiments, a cartridge 12 contains a label 290 indicating the test menu type and the test and / or analytical result. Cartridge ID Optics

[00247] In some embodiments, a reader 14 detects the cartridge type 12 using an optical reading of the cartridge device label, as explained in this document. For example, the cartridge type 12 can be detected using a static ID procedure or a dynamic ID procedure. Static ID

[00248] In some modes, the static ID mode is used as a barcode to identify what type of 12-gauge cartridge is in the cartridge. Petition 870250102472, dated 10 / 11 / 2025, p. 76 / 197 71 / 97 being used (i.e., with the corresponding reagents, buffers and / or lyophilized spheres) so that the reader 14 can perform the appropriate test sequence(s) and routine(s) for the type(s) of assay(s) being performed. In some embodiments, the static ID mode is used to identify a specific cartridge 12, such as a specific test panel. In some embodiments, a static identification label 290 may include printed optical targets 296 (or label markers 296 or identification markers 296). In some embodiments, the optical targets 296 (or printed marks 296) alter the reflection of an illumination LED whose wavelength is beyond the cutoff of the long-pass detector. Examples of optical targets 296 (or printed marks 296) are shown printed as black circles in Figure 29 and black rectangles in Figure 30.In some embodiments, a photodetector 144, 162 located adjacent to the illumination LED (e.g., 158, 146) detects the presence of a label mark 296 (or printer mark 296). The corresponding array of optical targets 296 (or printed mark 296) comprises a barcode or unique signature. The reflection measurement sequence is shown in Figures 23B and 24A.

[00249] In some embodiments, a cartridge 12, in connection with the reader 14, uses one or more specific label patterns to identify a specific cartridge 12. An exemplary label pattern for respiratory diseases is shown in Figure 29. Figure 28 shows exemplary label embodiments including a traditional 1D barcode reference method (Figure 28A) using a conventional barcode 298 (which can be read in connection with a conventional barcode scanner). Position detection

[00250] In some embodiments, a 12-gauge cartridge incorporates a position detection feature 302, 304. An example of the mes Petition 870250102472, dated 10 / 11 / 2025, p. 77 / 197 72 / 97 mo is shown in Figure 28B. A position detection feature 302, 304 is useful and helpful in determining that cartridge 12 is properly and fully inserted into reader 14. Such a feature 302, 304 can be employed as a check (after cartridge 12 is inserted) that a positive condition is met. In some embodiments, a position detection feature 302, 304 is enabled by optical targets 302, 304. In some embodiments, a detection feature 302, 304 is a target located slightly above the centerline of the adjacent reaction chamber 106. In some embodiments, a detection feature 302, 304 is slightly below the centerline of the horizontal axis of its adjacent reaction chamber 106. Examples thereof are shown in Figure 28B. In operation, the LED (e.g., red LED 158) in Figures 19A and 19B is located on the center line of the reaction chamber 106 and the photodiode 144 (or phototransistor 162).For optical module 140 to determine that cartridge 12 is fully inserted in the correct position, system 10 measures a reflection from both optical targets 302, 304). If cartridge 12 is located too high or too low (vertical axis in the figure), only one condition will be met. Therefore, an insertion failure can be detected. The configuration and system are capable of measuring the position to a resolution of approximately 0.010 inch when properly calibrated.

[00251] Referring again to Figure 28B, a first position detection feature 302 is located slightly above the centerline of an adjacent reaction chamber 106A. Similarly, cartridge 12 (in connection with label 290) may include a second position detection feature 304 located slightly above the centerline (i.e., horizontal centerline) of an adjacent reaction chamber 106B. Each of the first and second position detection features 302, 304 may include, Petition 870250102472, dated 10 / 11 / 2025, p. 78 / 197 73 / 97 comprise or be a geometric shape of a hue or color on top of a background surface or label area 290 of a different hue or color, such that the contrast between the position detection features 302, 304 and the background is visible or detectable through photodiode 144 (or phototransistor 162). For example, in the embodiment of Figure 28B, the position detection features 302, 304 include black rectangles on a white background. In the embodiment of Figure 28C and Figure 28D, the position detection features 302, 304, as well as the printed optical targets 296 (or label markers 296, or identification markers 296) may include a circle, an octagon, a square with rounded corners and / or other suitable shapes.For a correct position signal to be processed by the microprocessor (i.e., in the reader), the first position detection feature 302 must be identified as being above the centerline of the reference reaction chamber 106A, while the second position detection feature 304 must be identified as being below the centerline of the reference reaction chamber 106B. If both the first and second position detection features 302, 304 are below or above the centerlines of the reference reaction chambers 106A, 106B, cartridge 12 will not be detected as being in the correct position and further algorithms and routines will not proceed.In contrast to the relative positions of the first and second position detection features 302, 304 and still with reference to Figure 28B, the other printed optical targets 296 (or label markers 296 or identification markers 296) can be aligned with the respective center lines of the adjacent reaction chambers 106.

[00252] Figures 28C and 28D illustrate cartridges 12 with two different static ID patterns. In the cartridge of Figure 28C, the other printed optical targets 296 (or label markers 296, or mark) Petition 870250102472, dated 10 / 11 / 2025, p. 79 / 197 74 / 97 identification markers 296) are in different positions than in Figure 28D. For example, in the embodiment of Figure 28C, the cartridge includes 6 identification markers 296, while the embodiment of Figure 28D includes 5 identification markers 296. Furthermore, some of the identification markers 296 in Figure 28C are in different positions than in Figure 28D and vice versa. With eight (8) potential positions for the identification markers 296, and anywhere from 0 to 8 identification markers 296 possible for inclusion in a given cartridge, there are 8 factorial identifications (plus 1) or 40,321 potential identifications that can be encoded on label 290 using the identification markers 296. Dynamic ID

[00253] In some embodiments, a cartridge 12 can be identified in dynamic ID mode, that is, while the cartridge 12 is in motion when it is being inserted into a reader 14. In some embodiments, a cartridge 12 comprises an ID identification label 290. An example ID identification label is shown in Figure 30. In some embodiments, an ID identification label 290 comprises a first barcode optical target pattern 306 and / or a second barcode optical target pattern 308, in addition to one or more static identification markers 296.

[00254] In operation, the LEDs (e.g., red LEDs 158, as shown in Figures 19A and 19B) are constantly illuminated during the cartridge insertion step. In some embodiments, this is enabled via software control. During insertion (downward vertical movement of cartridge 12 on the vertical axis), the optical target barcode patterns 306, 308 of Figure 30 are illuminated by LEDs (e.g., red LEDs 158) and the resulting optical signature is detected by photodetectors 144, 162 (e.g., as shown in Figures 19A and 19B), forming the Petition 870250102472, dated 10 / 11 / 2025, page 80 / 197 75 / 97 yes a dynamic detection system that detects the identification of cartridge 12 while it is moving using the photodetectors 144, 162 already present in reader 14.

[00255] An exemplary design scheme of the LED drive circuit 280 and components is shown in Figure 31. In some embodiments, the LED drive circuit 280 may include the eight (8) LEDs 146 (or 158, as the case may be) arranged in parallel between a voltage source 278 (e.g., a 5-volt source) and ground 282, each of the LEDs 146 being positioned downstream of a corresponding resistor 276. In some embodiments, the adjacent photodetectors 144, 162 above the reaction chambers 106 measure the reflection intensities. In some embodiments, photodetectors 144, 162 are multiplexed at a frequency high enough to resolve the insertion speed of cartridge 12. Typically, the top row of reaction chamber 106 and detectors 144, 162 is used when this row detects the label barcode 306, 308 first (by insertion from the top).In some embodiments, the first 306 barcode optical target pattern and the second 308 barcode optical target pattern are the same. In some embodiments, the first 306 barcode optical target pattern and the second 308 barcode optical target pattern are different. It is further noted that a 306 or 308 pattern could be a timing marker of equally spaced marks to measure cartridge speed 12, should it prove to facilitate software identification. In other words, one of the patterns (i.e., first 306 barcode optical target pattern or second 308 barcode optical target pattern) could be the same each time and therefore used to assess how quickly cartridge 12 is being inserted into the reader 14. The other pattern (i.e., first 306 barcode optical target pattern) Petition 870250102472, dated 10 / 11 / 2025, p. 81 / 197 76 / 97 306 or second optical target barcode pattern 308) could then be used as an actual identifier representing the type of cartridge 12 being inserted. In some embodiments, the insertion speed information of the first pattern (i.e., the timing pattern or barcode, e.g., first optical target barcode pattern 306) can be used to calibrate the optical signature of the second pattern (i.e., the identification barcode, e.g., second optical target barcode pattern 308) so that the proper spacing between the barcode bars can be adjusted and / or corrected as needed to ensure accurate interpretation of the cartridge identification.The identification markers 296, the position detection features 302, 304 and the optical barcode target pattern 306, 308 (i.e., shown in Figures 28-30 and 32) allow the cartridges 12 to be properly identified by the reader 14 and correctly positioned within the reader 14, without the need for a barcode scanner, making use of photodetectors 144, 162 that are already present in the reader 14.

[00256] With further reference to Figures 28-30 and 32, once the identification of a cartridge 12 has been determined, the reader 14 will automatically execute the routines and sequences corresponding to the specific cartridge 12 in question. The identification of cartridge 12 determines which set of internal sequences (via software) is executed by the reader. In some embodiments, the reader 14 is Wi-Fi (i.e., network or internal) enabled so that software updates can be implemented (i.e., uploaded remotely and installed on the reader 14) to allow new and / or updated assays to be run on the reader 14 (i.e., using the same reader 14 hardware), in some cases with newly developed disposable cartridges 12 (e.g., to allow specific assays). Petition 870250102472, dated 10 / 11 / 2025, page 82 / 197 77 / 97 strains (i.e., new strains) of various viruses are run through the same underlying system. Cartridge ID with ambient light blocking label

[00257] In some embodiments, a cartridge 12 comprises a label 312 with a colored or shaded background. In some embodiments, a cartridge 12 comprises a dark or opaque label background 312. An example of a dark or opaque label background 312 is shown in Figure 32.

[00258] The shaded or colored label 312 provides ambient light blocking properties. When used, the barcode optical target features 296 may be alternate colors, transparent or white 314, in order to allow for changes in reflection that the photodetector 144, 162 can measure. The cartridge 12 may also include a cartridge name label 316 (i.e., a second label different from the first label 290, 312).

[00259] In some embodiments, an LED used for fluorescence excitation has certain spectral emission characteristics. Figure 34 shows an emission spectrum of a fluorescence excitation LED. In some embodiments, it is important that a lighting pattern contains a narrow beam for maximum energy transfer in the excitation of the reaction chamber fluid 106. Typical half-angle emission patterns are in the range of 5 to 10 degrees for typical total viewing angles of 20 degrees. In some embodiments, an LED may be an XZCBD78W LED by SunLED. There are several alternative part numbers that can also be used that are in the categories of surface mount, InGaN emitting material, narrow cone angle beam pattern, and high intensity output.

[00260] In some embodiments, a 12 cartridge comprises a filter. In some embodiments, an optical module comprises a Petition 870250102472, dated 10 / 11 / 2025, page 83 / 197 78 / 97 filter. In some embodiments, a filter is a long-pass fluorescence filter. In some embodiments, a filter has a centerline cutoff of about 520 nm. In some embodiments, a long-pass fluorescence filter is used to measure a reaction fluid labeled with FAM. Optical module 140 uses this and / or other gel, film, or plastic filters instead of a traditional dichroic glass filter, which can be too expensive to be practically useful in reader 14 and in the product concept developed in connection with this disclosure. In some embodiments, a filter is a Kodak Wratten 12 filter with a centerline cutoff of about 520 nm. In some embodiments, a separate filter may be disposed on the outer surface of each reaction chamber dome. In some embodiments, a filter may be disposed over more than one reaction chamber.

[00261] Figure 33 shows an emission spectrum of a red illumination LED. In some embodiments, an illumination pattern contains a narrow beam for enhanced performance. Typical half-angle emission patterns are in the range of 5 to 10 degrees. In some embodiments, a red illumination LED is a Vishay Semiconductor VLDR1235G LED and can emit light in a wavelength range of about 600 nm to about 660 nm.

[00262] Figure 34 shows the emission spectrum of an alternative lighting LED that emits light with wavelengths in the near-infrared in a range of about 730 nm to about 900 nm and centered at about 865 nm. In some embodiments, a lighting pattern contains a narrow beam for optimal performance. In some embodiments, the near-infrared lighting spectrum is within a range not visible to the human eye (e.g., in a range of about 730 nm to about 900 nm). Petition 870250102472, dated 10 / 11 / 2025, p. 84 / 197 79 / 97 nm and / or wavelengths above 700 nm). Typical half-angle emission patterns are in the range of 5 to 10 degrees. In some embodiments, an LED is an OSRAM Opto Semiconductors GmbH 4059-QS SFH LED. In some embodiments, the photodetectors 144, 162 described in this document include dual-mode photodetectors or tri-mode photodetectors (i.e., dual / tri-mode photodiodes 144 and / or dual / tri-mode phototransistors 162) capable of being calibrated to measure wavelengths in the ranges shown in Figure 33 (i.e., 600 nm to 660 nm), Figure 34 (i.e., 730 nm to 900 nm) and / or Figure 17 (i.e., 400 nm to 640 nm). Therefore, in some embodiments, the photodetectors 144, 162 described herein can be calibrated to measure wavelengths in a range of about 400 nm to about 900 nm.

[00263] Figure 35 shows one embodiment of the prototype design. Figure 35 illustrates a side view in section showing the cartridge 12 and its interface with the heating element 126, the heater spreader 128 and the optical module 140.

[00264] Figure 19A shows a detailed PCBA layout of the optical module. The improved optical signal-to-noise ratio is achieved by placing the optical components relative to the cartridge reaction chamber 106 shown in Figure 35. In some embodiments, and as shown in Figure 36 (enlarged view of a portion of Figure 35), a photodiode 144 is located directly above the volume of the reaction chamber 106, so that maximum photographic energy is collected from the fluorescent emission. In some embodiments, a 460 nm blue excitation LED 146 is placed as close as possible so that the maximum output energy of the narrow beam (e.g., 20-degree cone angle) enters and excites the reaction mixture in the reaction chamber 106. An optical shield 122 can be used to prevent scattered excitation light from entering the photodiode. Petition 870250102472, dated 10 / 11 / 2025, p. 85 / 197 80 / 97 144 from the side or through unwanted reflections. In some embodiments, a 144 photodiode incorporates a 160 filter (shown in Figures 19A and 19B) on the upper surface by means of an optical epoxy mounting method or similar.

[00265] In the embodiments shown in Figures 35 and 36, the photodetector may include a photodiode 144 as shown or a phototransistor 162. As shown in Figure 36, the optical module 140 may include a recessed portion 164 with a concave contour to match the outer shape of the reaction chamber domes (or hemispheres) 106. The recessed portion 164 may be disposed on the printed circuit board (PCBA) 150. When the cartridge 12 is inserted into the reader 14, in some embodiments, it is inserted vertically (i.e., in a downward direction, i.e., off-page in the view of Figures 35 and 36) and then pushed laterally (i.e., upwards in the view of Figures 35 and 36), so that the reaction chambers 106 are close to the optical module 140 and so that the heating elements 116, 126 and the heat spreaders 118, 128 are placed near or in contact with cartridge 12), as described in connection with the description of Figures 13 and 14.Therefore, when cartridge 12 is pushed laterally through the mechanical assembly 50, the domes (or hemispheres) of each of the reaction chambers 106 are brought into each of the corresponding recesses 164 arranged in the PCBA 150. Once cartridge 12 is correctly positioned within the reader 14, so that the dome of the reaction chamber 106 is at least partially protruding from the arc of the recessed portion 164, as shown in Figure 36, a spacing 328 of about 1 mm to about 4 mm (e.g., about 2 mm to about 3 mm) is maintained between the top of the dome of the reaction chamber 106 and the central point of the recessed portion 164. Petition 870250102472, dated 10 / 11 / 2025, page 86 / 197 81 / 97

[00266] In some embodiments, the dome (or hemisphere) of the reaction chamber 106 is concentric within the recessed portion 164 when correctly inserted. In some embodiments, the dome (or hemisphere) of the reaction chamber 106 is composed of a transparent polycarbonate, such as COC and / or COP (cyclic olefin copolymer and cyclic olefin polymer). The arrangement described in this document with respect to Figures 35 and 36 has been shown to result in an improved signal-to-noise ratio with respect to fluorescence detection. For example, the present embodiments do not include or require a lens, due to the placement of the enclosed reaction chamber 106 in both the light sources (i.e., LEDs 146, 158) and the photodetectors 144, 162. Therefore, the optical assembly 140 of the present embodiments can be less expensive and less complex than other comparable systems due to the lack of need for an optical lens.

[00267] In the embodiment of Figure 36, the optical shielding prevents the light emitted by the LED from being directly detected by the photodetector. After activating the biological solution in the reaction chamber, the photodetector detects the activation solution. Due to the photodetector's location in close proximity to the reaction chamber, an optical lens is not required. In some embodiments, a first LED 158 (e.g., red LED) in Figures 19A and 19B is placed on one side of a photodiode 144, while a second LED (e.g., a 460 nm (blue) LED 146) is placed on another adjacent side of photodiode 144, so that the first LED 158, photodiode 144, and the second LED 146 form a 90-degree angle. In some embodiments, an LED placement (e.g., red LED 158) is also in a horizontal line with photodiode 144 and positioned so that it is between adjacent reaction chambers.This allows for the printing of an optical target with barcode 296 on a label 290 in an available space on the surface of cartridge 12. Petition 870250102472, dated 10 / 11 / 2025, p. 87 / 197 82 / 97 does not interfere with hydrophobic openings 108 (i.e., ventilation membranes 108). The location of the red LED 158 also allows and enables alignment for dynamic ID detection during cartridge insertion 12, which can be advantageous.

[00268] In some embodiments, a 144 photodiode is a TEMD5020X01 photodetector by Vishay Semiconductors. Note that other 144 photodiodes or 162 phototransistors (and associated components) can also be used as the 144, 162 photodetector element, provided size and cost constraints are met, which improves feasibility for home testing.

[00269] Figure 43 illustrates a side view of the reaction chamber assembly in an alternative configuration, according to aspects of the present embodiments. In the embodiment of Figure 43, at least one of the LEDs (e.g., the blue LED 146) is integrated into the cartridge 12 so that it is positioned immediately below the reaction chamber 106 to increase the excitation of the nucleic acids contained therein. The presence of the LED 146 disposed within the cartridge 12 would require a space, hole, and / or void in the cartridge 12, potentially decreasing heat transfer to the reaction chamber 106. In some embodiments, the LED 146 includes a smaller diameter than that of the reaction chamber 106, thus allowing a ring 334 surrounding the LED 146 where the reaction chamber 106 comes into direct contact with the cartridge material 12, to encourage heat transfer to the reaction chamber 106.Alternatively, or additionally, inefficient LEDs can be used (i.e., LEDs that consume additional current and emit more thermal energy) so that the LED itself can act as a heat source in maintaining the temperature of the reaction chamber 106 at or around 60 degrees C during amplification. High-speed cartridge ID mode Petition 870250102472, dated 10 / 11 / 2025, page 88 / 197 83 / 97

[00270] Figure 24A shows an alternative embodiment of the cartridge ID timing sequence. In some embodiments, a cartridge ID timing sequence uses 4 excitation LEDs instead of 8. This provides an advantage of being able to scan (photodetector multiplexing) at a faster rate (high speed). This can be advantageous when a user inserts cartridge 12 into reader 14 very quickly. The high-speed mode can be used in static or dynamic ID detection. C. Sample Collection

[00271] In some embodiments, the present disclosure provides one or more parts for collecting a sample (i.e., a sample collection container, for example, a container or vial 18). In some embodiments, a sample collection container 18 is used to collect and / or contain a sample. In some embodiments, a sample collection container 18 comprises one or more target nucleic acids. In some embodiments, a sample collection container 18 comprises one or more parts that interface with a cartridge 12. In some embodiments, a sample collection container 18 is sample-specific. In some embodiments, a sample collection container 18 is assay-specific.

[00272] In some embodiments, a sample collection container 18 comprises a sterile swab 16 and a buffer / reagent container. D. Detection System

[00273] In some embodiments, the present disclosure provides a detection system 10. An exemplary detection system is shown in Figure 1. The system 10 is designed for use by untrained users (consumers) and incorporates simple and familiar tasks whenever possible. The detection system 10 is designed to operate in a domestic environment. In some embodiments, the system Petition 870250102472, dated 10 / 11 / 2025, page 89 / 197 The 84 / 97 mA detection system uses only standard wall power (e.g., 110 V AC, using a commercially available USB charger). The system architecture (such as cartridge, reader, and assay reagents) provides a flexible and expandable system, allowing for the addition and development of new applications and measurement menus / functionalities. In some embodiments, the system (i.e., reader) consumes approximately 100 mA to approximately 1000 mA of current when powered by the USB charger. In some embodiments, the system includes a lithium-ion battery (e.g., rechargeable battery, non-rechargeable battery) to power the device, enabling portability and use when AC power is unavailable (e.g., in locations without power access, during power outages, etc.). E. Nucleic Acid Detection

[00274] In some embodiments, systems, methods, compositions, or devices provided in this document detect one or more target nucleic acids. In some embodiments, a target nucleic acid is deoxyribonucleic acid (DNA). In some embodiments, a target nucleic acid is ribonucleic acid (RNA). In some embodiments, a target nucleic acid is single-stranded. In some embodiments, a target nucleic acid is double-stranded.

[00275] In some embodiments, a target nucleic acid is present in a sample. In some embodiments, a sample comprises one or more target nucleic acids. In some embodiments, a sample comprises one or more target nucleic acids and nucleic acids other than one or more target nucleic acids. In some embodiments, a target nucleic acid is from a eukaryote. In some embodiments, a target nucleic acid is from a prokaryote. In some embodiments, a target nucleic acid is a parasite (e.g., protozoan). Petition 870250102472, dated 10 / 11 / 2025, p. 90 / 197 85 / 97 (ary), bacterial, viral, or fungal. In some modalities, a target nucleic acid is from a human being.

[00276] In some embodiments, a sample is an environmental sample. In some embodiments, a sample is a biological sample. In some embodiments, a biological sample is a sample obtained or derived from a biological source (e.g., a tissue or organism or cell culture) of interest. In some embodiments, a source of interest is or comprises an organism, such as an animal or human. In some embodiments, a biological sample is or comprises biological tissue or fluid.In some embodiments, a biological sample may be or comprise bone marrow; blood; blood cells; ascites; tissue or fine-needle biopsy samples; body fluids containing cells; free-floating nucleic acids; sputum; saliva; urine; cerebrospinal fluid; peritoneal fluid; pleural fluid; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washes or rinsings, such as ductal washes or bronchoalveolar washes; aspirates; scrapings; bone marrow specimens; tissue biopsy specimens; surgical specimens; feces; other body fluids, secretions and / or excretions; and / or cells thereof, etc. In some embodiments, a biological sample is or comprises cells obtained from an individual. In some embodiments, the cells obtained are or include cells from an individual from whom the sample is obtained.In some modalities, a sample is a primary sample obtained directly from a source of interest by any appropriate means. For example, in some modalities, a primary biological sample is obtained by methods selected from the group consisting of biopsy (e.g., fine needle aspiration or tissue biopsy), surgery, collection of body fluid (e.g., blood, lymph, feces, etc.), etc. Petition 870250102472, dated 10 / 11 / 2025, page 91 / 197 86 / 97

[00277] In some embodiments, the cells in a sample are lysed to release nucleic acids. In some embodiments, the cells in a sample are lysed within a composition or device, as provided in this document. In some embodiments, the cells in a sample are lysed by heating the sample. In some embodiments, the cells in a sample are lysed by heating the sample to about 80 °C, 85 °C, 90 °C, or 95 °C.

[00278] In some embodiments, the systems, methods, compositions, or devices provided in this document comprise the amplification of a target nucleic acid. One skilled in the art will recognize various methods known in the art for amplifying nucleic acids. In some embodiments, the systems, methods, compositions, or devices provided in this document comprise isothermal nucleic acid amplification.In some embodiments, isothermal amplification may be nucleic acid sequence-based amplification (NASBA), recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), strand displacement amplification (SDA), helicase-dependent amplification (HDA), or cleavage enzyme amplification reaction (NEAR). In certain example embodiments, non-isothermal amplification methods may be used, including but not limited to polymerase chain reaction (PCR), multiple displacement amplification (MDA), rolling circle amplification (RCA), ligase chain reaction (LCR), or branching amplification method (RAM). In some embodiments, isothermal amplification is LAMP, for example, as described in US patents 9,909,168; US 7,374,913; US 7,851,186; and US 7,846,695. In some embodiments, the isothermal amplification is condensed LAMP (cLAMP), for example, as described in US 63 / 470,298 and US 63 / 511.491. In some modes, isothermal amplification occurs at approximately 50. Petition 870250102472, dated 10 / 11 / 2025, p. 92 / 197 87 / 97 °C, 55 °C, 60 °C, 65 °C or 70 °C. In some forms, LAMP occurs at approximately 50 °C, 55 °C, 60 °C, 65 °C or 70 °C. In some forms, LAMP or cLAMP occurs at room temperature (e.g., ambient temperature).

[00279] A person skilled in the art is aware of various technologies useful in detecting one or more target nucleic acids. In some embodiments, the detection technologies comprise, for example, absorbance, CRISPR / Cas detection (e.g., SHERLOCK), FRET or bridging (e.g., INSPECTR as described in WO2020037038A1, the full content of which is incorporated herein by reference).

[00280] Certain CRISPR / Cas enzymes have been identified that have the ability to non-specifically cleave collateral nucleic acid(s) when activated by binding to a target site on a target nucleic acid recognized by the guide RNA with which the CRISPR / Cas enzyme is complexed. Representative examples of Cas12, Cas13, and Cas14 enzymes have demonstrated such collateral cleavage activity. See, for example, Swarts and Jinek, Mol. Cell. February 7, 2019; 73(3): 589-600.e4; Harrington LB et al., Science 2018; 362: 839-842; Li SY et al. Cell Res. 2018; 28: 491-493; Chen JS et al., Science 2018; 360: 436-439; Abudayyeh OO et al., Science 2016; 353aaf5573; East-Seletsky A. et al., Nature 2016; 538: 270-273; Gootenberg JS et al., Science 2017;356:438-442; Myhrvold C., et al., Science 2018;360:444-448; and Gootenberg JS et al., Science 2018; 360:439-444. Some collateral cleavage activity of the CRISPR / Cas enzyme digests or cleaves single-stranded nucleic acids.Some collateral cleavage activity of the CRISPR / Cas enzyme digests or cleaves double-stranded nucleic acids. Some collateral cleavage activity of the CRISPR / Cas enzyme digests or cleaves RNA. Some collateral cleavage activity of the CRISPR / Cas enzyme digests or cleaves DNA. Petition 870250102472, of 10 / 11 / 2025, p. 93 / 197. 88 / 97 The collateral cleavage activity of the CRISPR / Cas enzyme digests or cleaves both RNA and DNA. This collateral activity has been leveraged to develop CRISPR / Cas detection technologies (e.g., diagnostics) that achieve the detection of nucleic acids containing the relevant target site (e.g., Cas target nucleic acid), or its complement, in biological and / or environmental sample(s). See, for example, Gootenberg, JS et al., Science 2017, 356 (438-442); WO2019 / 011022; US Patents 10,494,664; 10,337,051; and 10,266,887; sherlock.bio / better-faster-affordable-diagnostic-testing.

[00281] SHERLOCK is a detection technology comprising the steps of: contacting a CRISPR / Cas complex comprising a Cas protein with collateral cleavage activity, a guide RNA selected or manipulated to be complementary to a target nucleic acid (e.g., a Cas target nucleic acid sequence), and a sample potentially comprising a Cas target nucleic acid (see, for example, WO 2018 / 107129, WO 2019 / 011022, which are incorporated herein by reference). In some embodiments, CRISPR / Cas-based detection may be a CRISPR / Cas13-based detection system. In some embodiments, a CRISPR / Cas-based detection system is a CRISPR / Cas12-based detection system. In some embodiments, a CRISPR / Cas13 or CRISPR / Cas12-based detection system is a SHERLOCK detection system. A person skilled in the art is aware of various CRISPR / Cas enzymes that may be useful in the systems, compositions, and methods as provided in this document.For example, CRISPR / Cas enzymes are described in WO2016 / 166340; WO2016 / 205711; WO / 2016 / 205749;. WO2016 / 205764; WO2017 / 070605; WO / 2017 / 189308; WO2021 / 154866A1; WO2023 / 009526, the entire content of each of which is incorporated into this document by reference. In some Petition 870250102472, dated 10 / 11 / 2025, page 94 / 197 In embodiments 89 / 97, the SHERLOCK detection technology also comprises a detectably labeled nucleic acid probe. Cleavage of the detectably labeled nucleic acid probe by the collateral cleavage activity of a CRISPR / Cas enzyme can induce or enhance the detectable label indicating the presence of a target nucleic acid. In some embodiments, a detectably labeled nucleic acid probe is labeled with a fluorescent label. In some embodiments, a fluorescent label comprises a fluorescent group at the 5' end and a quencher group at the 3' end. In some embodiments, a fluorescent group is hexachlorofluorescein (HEX) or carboxyfluoroscein (FAM). In some embodiments, a quencher group is a black hole quencher (BHQ).

[00282] In some embodiments, the detection of one or more nucleic acids comprises obtaining a biological sample from a subject through a sample container (see, for example, Figures 1-5); incubating the biological sample with at least one of a reagent and a buffer through the sample container, thereby producing a biological solution; inserting the sample container into a cartridge so that the biological solution flows into an internal chamber of the cartridge, the internal chamber comprising a first heating zone; inserting the cartridge into an electronic reader comprising multiple heating elements to create the first heating zone and a second heating zone within the cartridge; performing a lysis step on the biological solution within the first heating zone;Passively cool the biological solution by opening an internal passage in the cartridge so that the biological solution flows via gravity feed into the internal passage, the internal passage being fluidly downstream and vertically below the internal chamber; amplify one or more target nucleic acids in the biological solution; Petition 870250102472, dated 10 / 11 / 2025, pp. 95 / 197 90 / 97 by isothermal amplification within the second heating zone comprising multiple reaction chambers fluidly downstream of the internal passage; wherein each of the multiple reaction chambers comprises: a CRISPR / Cas enzyme with collateral cleavage activity, a guide RNA that specifically hybridizes with a target nucleic acid, a detectably labeled nucleic acid probe, wherein hybridization of the guide RNA with the target nucleic acid induces or enhances the collateral cleavage activity of the CRISPR / Cas enzyme and the CRISPR / Cas enzyme cleaves the detectably labeled nucleic acid probe, wherein cleavage of the detectably labeled nucleic acid probe results in an increase in detectable labeling, illuminating the biological solution within each of the multiple reaction chambers through a plurality of optical energy sources,Each of the multiple optical energy sources is arranged in the vicinity of one of the multiple reaction chambers, determining the presence of at least one target nucleic acid within the biological solution based on the presence or level of detectable labeling using a detection device (Figure 28). F. Method and Use

[00283] With reference to Figure 37, in some embodiments, the present disclosure provides a method 1600 for detecting one or more target nucleic acids using a reader 14, a cartridge 12, a sample collection or a combination thereof. In some embodiments, the methods according to this disclosure comprise one or more of the following steps: I collect a sample; ii. thermally lyse the cells in the sample; iii. Passively cool the sample; iv. transfer to one or more reaction chambers; Petition 870250102472, dated 10 / 11 / 2025, pp. 96 / 197 91 / 97 v. amplify isothermally; vi. activate the Cas enzyme; and vii. detect.

[00284] For example, as shown in Figure 37 and as described in this document, in step 1602, method 1600 may include providing a biological sample (e.g., saliva, mucus, etc.) by the subject. In step 1604, method 1600 may include incubation of the sample with reagent / buffer. In step 1606, method 1600 may include thermal lysis of cells in the sample-reagent mixture. In step 1608, method 1600 may include passive cooling of the sample-reagent mixture after lysis (e.g., while the sample moves (i.e., flows) between the lysis chamber 94 and the reaction chambers 106). In step 1610, method 1600 may include isothermal amplification in the reaction chambers 106. In step 1612, method 1600 may include detection of the target nucleic acid.

[00285] The total workflow for the test takes approximately 20 to 40 minutes, depending on the test being run. The user steps to initiate the test execution are less than 2 minutes, and the remainder of the test is executed automatically. Figure 3 shows a combined summary of the user workflow and the test workflow.

[00286] In some embodiments, a sample is collected. In some embodiments, a user collects a sample from themselves using a standard sterile swab 16. Alternatively, an adult may collect a nasal swab sample from a child or other subject.

[00287] In some embodiments, a sample is eluted into a buffer. In some embodiments, a user opens a buffer tube and rotates a swab head to elute the sample into a buffer. Alternatively, a standard extraction tube may be used for elution.

[00288] In some embodiments, a sample is transferred to Petition 870250102472, dated 10 / 11 / 2025, pp. 97 / 197 92 / 97 a cartridge. In some embodiments, a buffer containing a sample is supplied through a sample inlet port. An exemplary transfer is shown in Figure 5. In some embodiments, a cap is used to seal the cartridge. An exemplary cap is shown in Figure 5. After a sample is added to a cartridge, the cartridge is inserted into a reader.

[00289] In some embodiments, a reader automatically provides fluidic control, thermal control, and optical measurement of cartridge 12 within a test time of 15 to 45 minutes (e.g., 20 to 40 minutes). After the test is complete, a result is displayed using easy-to-read LEDs (e.g., the LED lights up for a positive result). In some embodiments, cartridge 12 contains a label indicating the test type and the assay and / or analytical result.

[00290] In some embodiments, a cartridge 12 is inserted into a reader 14. In some embodiments, inserting a cartridge 12 into the reader 14 initiates a detection method. An exemplary installation of cartridge 12 is shown in Figure 6.

[00291] In some embodiments, a reader 14 automatically detects the presence of a cartridge 12. In some embodiments, a reader 14 automatically detects the type of cartridge 12.

[00292] In some embodiments, a reader 14 communicates its status (e.g., On / Off, Ready / Running / Complete, Invalid Result or Error) by LEDs. In some embodiments, the LEDs are positioned adjacent to the corresponding label 290. In some embodiments, the label 290 is on the housing (i.e., the outer surface of the reader 14). An example of a status LED scheme is shown in Figure 7.

[00293] In some modes, the temperature is configurable using software. In some modes, the step time is configurable via software. In some modes, one se Petition 870250102472, dated 10 / 11 / 2025, pp. 98 / 197 93 / 97 execution sequence comprises a warm-up cycle and an amplification cycle. Cell lysis in the sample

[00294] In some embodiments, a method according to the present invention comprises a sample heating step. In some embodiments, a sample is heated to lyse cells in the sample. In some embodiments, a heating cycle leads to cell lysis in the sample. In some embodiments, a sample is heated to at least 80 °C, such as at least 85 °C, such as 90 °C. In some embodiments, a sample is heated in a lysis chamber 94 in cartridge 12.

[00295] In some embodiments, an area of ​​the lysis chamber 94 of the cartridge (Figure 8) is heated (e.g., to 90 °C) by the reader 14 for the duration defined by the test sequence. In some embodiments, an area of ​​lysis chamber 94 is then passively cooled to below 60 °C before the next step.

[00296] In some embodiments, a sample is transferred from the lysis chamber 94 to the reaction chambers 106. In some embodiments, a sample is being divided into individual reaction chambers 106. In some embodiments, a sample is transferred to one or more reaction chambers 106. In some embodiments, a sample is transferred to two or more reaction chambers 106. In some embodiments, a sample is transferred to three or more reaction chambers 106. In some embodiments, a sample is transferred to four or more reaction chambers 106. In some embodiments, a sample is transferred to five or more reaction chambers 106. In some embodiments, a sample is transferred to six or more reaction chambers 106. In some embodiments, a sample is transferred to seven or more reaction chambers 106. In some embodiments, a sample is transferred to Petition 870250102472, dated 10 / 11 / 2025, pp. 99 / 197 94 / 97 eight or more reaction chambers 106. In some embodiments, a reaction chamber 106 may comprise a volume in the range of about 10 μl to about 100 μl, such as in the range of 15 μl to about 80 μl, such as in the range of 20 μl to about 60 μl, such as in the range of 30 μl to about 50 μl, such as a 40 μl sample. In some embodiments, a sample transfer is driven by gravity flow (e.g., when a reader 14 and a cartridge 12 are positioned in a vertical orientation). An exemplary vertical orientation is shown in Figure 9.

[00297] In some embodiments, a detection system 10 uses the rehydration of a lyophilized sphere within each reaction chamber 106 to verify the filling of the reaction chamber. The filling of the chamber can be detected, for example, by a change in fluorescence that occurs when a lyophilized sphere 268 is rehydrated. Amplification cycle

[00298] In some embodiments, an amplification cycle is performed in the temperature range of about 50 °C to about 70 °C, such as about 55 °C to about 65 °C. In some embodiments, the amplification is performed under isothermal conditions.

[00299] In some embodiments, a reader 14 uses a film heater to heat the reaction chamber area 126 of the cartridge 12 to about 50 °C to about 70 °C, such as about 55 °C to about 65 °C, such as about 60 °C during amplification.

[00300] In some modes, the amplification is LAMP amplification. Detection

[00301] In some modes, an amplification product is detected. In some modes, a LAMP amplification product is detected. In some modes, an operating software Petition 870250102472, dated 10 / 11 / 2025, p. 100 / 197 95 / 97 final detects whether amplification has occurred for each reaction chamber. In some modes, detection is based on raw optical data. Figure 11 shows two examples of raw optical data plotted on a graph. Liquid samples of SARS-CoV-2 (Figure 11A) show amplification 318 in about 15 minutes, and negative control samples (Figure 11B) show no amplification after 60 minutes.

[00302] In some embodiments, the raw data are plotted for analysis in a standardised format that also captures key metadata from the run, such as instrument identification (reader 14), sample type and cartridge type 12 (see Figure 12). The displayed data may include assay reaction results 318 for each of the 8 channels, temperature profiles 320 for each of the two heating zones, fill detection signals 322 for each of the eight channels and ambient light monitoring 324 for each of the eight channels.

[00303] As shown in Figure 11A, the fill detection signals 322 may include a drop 330 in amplitude when fluid enters the reaction chambers 106 due to less light from the LEDs reaching the photodetectors 144, 162 when the reaction chambers 106 are filled with fluid. Furthermore, as shown in Figure 11B, the fill detection signals 322 may experience an increase 332 in magnitude when the cartridge is inserted due to increased reflectance. The fill detection algorithm 230, as shown in Figure 24B, verifies that the drop 330 in magnitude is observed in each (i.e., all 8) of the reaction chambers 106, thus confirming that all reaction chambers 106 are filled with fluid. As shown in legend 326 in Figure 12, each of the channels (i.e., reaction chambers 106) may contain or contain a lyophilized sphere corresponding to an indication. Petition 870250102472, dated 10 / 11 / 2025, page 101 / 197 96 / 97 different indication (for example, including, but not limited to: respiratory viruses, such as SARS-CoV-2 (SCV2), FluA-1, FluA-2, FluB, RSV (respiratory syncytial virus), as well as sexually transmitted infections (STIs), including Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV), as well as other potential indications, infections, bacteria and / or viruses. That is, each lyophilized sphere may contain reagents, primers for nucleic acids, enzymes, etc., which are specifically chosen to perform a particular assay to detect a particular indication. This arrangement allows multiple assays corresponding to multiple viruses or conditions to be performed simultaneously based on a single patient sample, having a different lyophilized sphere composition in each reaction chamber 106.

[00304] In some embodiments, a reader 14 displays the assay results. In some embodiments, a reader 14 displays the test results by means of illuminated LEDs. In some embodiments, the illuminated LEDs correspond to labels 290 on a cartridge 12. That is, each cartridge 12 may have different labels printed on it 290 corresponding to the conditions being tested in the cartridge 12, so that the labels are visible adjacent to the LEDs on the reader 14, so that the same LEDs on the reader 14 may indicate a variety of different conditions depending on which cartridge 12 is inserted. In some embodiments, a target nucleotide acid is detected in a reaction chamber 106, resulting in a positive result. In some embodiments, an assay that is considered positive will be indicated. Exemplary indication is shown in Figure 2.If no test is positive and the test execution is valid (including control reactions), the LED corresponding to 'NEG' (i.e., indicating that all tests are negative) will light up, as shown in Figure 2B. Petition 870250102472, dated 10 / 11 / 2025, p. 102 / 197 97 / 97 EXEMPLIFICATION Example 1:

[00305] The present Example demonstrates the detection of the SARS-CoV-2 virus using a detection system according to the present invention. Figure 11 shows two examples of raw optical data plotted on a graph. The vertical axis shows the optical signal at a photodetector in millivolts, while the horizontal axis shows the reaction time in minutes. Liquid samples containing SARS-CoV-2 (Figure 11A) show amplification at approximately 15 minutes (i.e., an increase in fluorescence), and the negative control samples (Figure 11B) show no amplification after 60 minutes (i.e., no increase in fluorescence). The eight optical signal channels in Figure 11A and Figure 11B correspond to signals measured by eight separate photodetectors, each corresponding to a different reaction chamber in a cartridge containing eight reaction chambers.Although the example shown here has the same detection assay (i.e., SARS-CoV-2) in each of the eight reaction chambers, in other examples each reaction chamber may present a different assay to detect a different target nucleic acid. EQUIVALENTS

[00306] Those skilled in the art will recognize, or will be able to verify using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. The scope of the present invention is not intended to be limited to the above description, but is as set forth in the following claims. Petition 870250102472, dated 10 / 11 / 2025, p. 103 / 197

Claims

1 / 19 CLAIMS 1. System for detecting the presence of a nucleic acid associated with at least one indication in a biological solution, characterized in that it comprises: an electronic reader for performing one or more assays and displaying the results thereof; a cartridge configured to be inserted into the reader, the cartridge comprising a cartridge assembly; and a sample collection container for collecting a biological sample and transferring it to an internal chamber of the cartridge.

2. System according to claim 1, characterized in that it further comprises an internal assembly comprising the cartridge assembly once the cartridge is inserted into the reader, the internal assembly further comprising: a heating unit comprising one or more heating elements; and an optical assembly comprising at least one LED and at least one photodetector. 3.System according to claim 2, characterized in that the cartridge assembly comprises a lysis chamber for receiving the biological sample from the sample collection container and one or more reaction chambers arranged fluidly downstream of the lysis chamber.

4. System according to claim 3, characterized in that one or more heating elements comprise a first heating element for maintaining the lysis chamber at a first temperature and a second heating element for maintaining the one or more reaction chambers at a second temperature.

5. System according to claim 3, characterized Petition 870250102472, dated 10 / 11 / 2025, p.104 / 197 2 / 19 by virtue of the cartridge assembly comprising: at least one of a buffer and a reagent disposed within the lysis chamber; at least one lyophilized lysis sphere disposed within the lysis chamber; and a lyophilized PCR sphere disposed within each of the one or more reaction chambers.

6. System according to claim 3, characterized in that each of the one or more reaction chambers comprises a transparent dome.

7. System according to claim 3, characterized in that the cartridge assembly comprises a polymer coating forming a rear surface of the cartridge and a film layer comprising a front surface of the cartridge, the polymer coating and the film layer each sandwiching the buffer, reagent, at least one lyophilized lysis sphere and / or lyophilized PCR sphere between them. 8.System according to claim 7, characterized in that the film layer comprises a polypropylene laminate.

9. System according to claim 1, characterized in that at least one LED comprises a first LED in optical communication with a reaction chamber of one or more reaction chambers, and wherein the at least one LED is configured to illuminate an interior of one or more reaction chambers.

10. System according to claim 9, characterized in that at least one LED comprises a second LED in optical communication with at least one identification marker disposed on a cartridge surface. Petition 870250102472, dated 10 / 11 / 2025, page 105 / 197 3 / 19 11. System according to claim 9, characterized in that at least one photodetector is configured to measure the fluorescence emitted from an illuminated interior of one or more reaction chambers. 12.System according to claim 1, characterized in that each of at least one LED and at least one photodetector is integrated into a printed circuit board assembly (PCBA).

13. System according to claim 12, characterized in that the heating unit is disposed adjacent to a front surface of the cartridge and the PCBA is disposed adjacent to a rear surface of the cartridge.

14. System according to claim 12, characterized in that the heating unit is integrated into the PCBA.

15. System according to claim 5, characterized in that one or more reaction chambers comprise multiple reaction chambers, and in which one type of lyophilized PCR sphere in a first reaction chamber of the multiple reaction chambers is different from one type of lyophilized PCR sphere in a second reaction chamber of the multiple reaction chambers. 16.System according to claim 5, characterized in that one or more reaction chambers comprise multiple reaction chambers and in that each of the multiple reaction chambers comprises a different type of lyophilized PCR sphere configured to be used in a different reaction.

17. System according to claim 5, characterized in that one or more reaction chambers comprise multiple reaction chambers and in that each of the multiple reaction chambers comprises the same type of lyophilized PCR sphere configured to be used in the same reaction.

18. System according to claim 3, characterized in that the light emitted from at least one LED excites at least one nucleic acid contained within one or more reaction chambers without passing through an optical lens. 19.System according to claim 2, characterized in that it further comprises a mechanical assembly, wherein the mechanical assembly is configured to move the cartridge laterally within the reader after the cartridge is inserted into the reader, after the closing of a reader cover, the mechanical assembly comprising: at least one linkage coupling the cover to an internal device disposed within the reader; and a cam coupled to at least one linkage and to the internal device, the cam converting the closing movement of the cover into lateral movement of the internal device.

20. System according to claim 1, characterized in that the cartridge comprises at least one identification mark configured to be illuminated by at least one LED.

21. System according to claim 20, characterized in that at least one identification mark comprises at least one printed barcode. 22.System according to claim 20, characterized in that at least one identification mark comprises one or more printed forms.

23. System according to claim 20, characterized in that at least one identification mark is printed in ink (for example, black ink, colored ink, or a combination of inks).

24. System according to claim 20, characterized in that at least one identification mark is associated with at least one indication. 25.A method for identifying an attribute of a cartridge configured to be inserted into an electronic reader, characterized in that it comprises: providing the electronic reader, the electronic reader comprising at least one internal LED, at least one internal photodetector and at least one internal microprocessor communicatively coupled to at least one photodetector and at least one LED; providing the cartridge, the cartridge comprising at least one identification mark; inserting the cartridge into the reader; illuminating, by at least one internal LED, at least one identification mark, thereby creating an illuminated identification mark; detecting, by at least one internal photodetector, an optical signature of the illuminated identification mark; and identifying, by at least one internal microprocessor, at least one attribute of the cartridge based on the illuminated identification mark. 26.Method according to claim 25, characterized in that the illumination of at least one identification mark occurs when the cartridge is inserted into the electronic reader.

27. Method according to claim 26, characterized in that at least one identification mark comprises at least one barcode.

28. Method according to claim 27, characterized in that at least one internal LED comprises at least one first LED and one second LED, wherein at least one barcode comprises: Petition 870250102472, dated 10 / 11 / 2025, p.108 / 197 6 / 19 a first barcode used to quantify the speed at which the cartridge is inserted into the electronic reader, the first barcode being illuminated by the first LED; and a second barcode used to identify at least one attribute of the cartridge, the second barcode being illuminated by the second LED, and wherein at least one microprocessor uses the quantified speed to calibrate the optical signature of the second barcode, thus allowing the cartridge attribute to be identified.

29. Method according to claim 25, characterized in that at least one internal photodetector comprises at least one of a photodiode and a phototransistor.

30. Method according to claim 25, characterized in that at least one internal LED comprises at least one of a red LED and a blue LED. 31.Method according to claim 25, characterized in that at least one internal photodetector comprises a dual-mode photodetector configured to measure the light emitted from at least one LED within a first spectrum and a second spectrum, and wherein the second spectrum does not overlap with the first spectrum.

32. Method according to claim 31, characterized in that the first spectrum comprises wavelengths in a range of about 600 nm to about 660 nm, and wherein the second spectrum comprises wavelengths in a range of about 730 nm to about 900 nm.

33. Method according to claim 25, characterized in that at least one identification mark comprises Petition 870250102472, dated 10 / 11 / 2025, page 109 / 197 7 / 19 and contains one or more marks printed on a label disposed on a surface of the cartridge. 34.A method according to claim 33, characterized in that at least one LED comprises from about 4 to about 12 identification LEDs, wherein one or more printed marks comprise from about 4 to about 12 printed marks, each printed mark being positioned to correspond to a position of one of the identification LEDs, such that the presence or absence of a printed mark at a position can be detected by the identification LED at the corresponding position.

35. A method according to claim 34, characterized in that the number of identification LEDs is greater than the number of printed marks.

36. A method according to claim 34, characterized in that a unique combination of marked positions on the label is associated with the cartridge attribute. 37.Method according to claim 25, characterized in that the attribute comprises one or more types of tests that can be performed using the cartridge.

38. Method according to claim 25, characterized in that at least one internal microprocessor executes one or more pre-loaded routines based on the attribute that is determined as a result of the method of identifying an attribute of a cartridge.

39. Method according to claim 33, characterized in that one or more printed marks comprise one or more position detection features.

40. Method according to claim 39, characterized in that one or more position detection features... Petition 870250102472, dated 10 / 11 / 2025, p.110 / 197 8 / 19 position comprise: a first position detection feature positioned on the label such that a center line of the first position detection feature is positioned so as to be slightly above a center line of a first reader component when the cartridge is correctly positioned within the reader; and a second position detection feature positioned on the label such that a center line of the second position detection feature is positioned so as to be slightly below a center line of a second reader component when the cartridge is correctly positioned within the reader; the method comprising determining, by the microprocessor, whether or not the cartridge is correctly positioned within the reader based on: 1) the position of the first position detection feature relative to the first reader component, e.g. 2) the position of the second position detection feature relative to the second reader component, wherein each of the first and second components comprises at least one internal photodetector and at least one internal LED.

41. Method according to claim 25, characterized in that the reader is configured to identify the cartridge attribute based on multiple operating modes, the multiple operating modes comprising: a static identification mode comprising the identification of the attribute, through at least one identification mark and the reader, after the cartridge is inserted into the reader; and Petition 870250102472, dated 10 / 11 / 2025, p. 111 / 197 9 / 19 a dynamic identification mode comprising the identification of the attribute, through at least one identification mark and the reader, while the cartridge is being inserted into the reader.

42. Method according to claim 33,characterized in that one or more printed marks are printed with ink (e.g., colored ink, black ink, and / or other color combinations) on the label on top of a background that is at least one of white and gray.

43. Method, according to claim 25, characterized in that the cartridge comprises at least one lyophilized sphere disposed thereof, at least one lyophilized sphere comprising at least one of a lyophilized lysis sphere and a lyophilized PCR sphere.

44. System, characterized in that it comprises the reader and the cartridge, according to claim 25.

45. Method, characterized in that it comprises: obtaining (or providing) a biological sample; incubating the biological sample with at least one of a reagent and a buffer,thus producing a biological solution; performing a lysis step in the biological solution; amplifying one or more target nucleic acids in the biological solution by isothermal amplification; incubating the biological solution with a composition comprising: a CRISPR / Cas enzyme with collateral cleavage activity; one or more guide RNAs each specifically hybridizing with one or more of the target nucleic acids; and a detectably labeled nucleic acid probe, Petition 870250102472, 10 / 11 / 2025, p. 112 / 197 10 / 19 wherein the hybridization of each of the guide RNAs with its respective target nucleic acid induces or enhances the collateral cleavage activity of the CRISPR / Cas enzyme and the CRISPR / Cas enzyme cleaves the detectably labeled nucleic acid probe,wherein the cleavage of the detectably labeled nucleic acid probe results in an increase in detectable labeling; and the determination of the target nucleic acid present in the biological sample is based on the detection of an increase in the detectable marker.

46. Method according to claim 45, characterized in that the lysis step comprises a thermal lysis step carried out at a temperature in a range of about 70 degrees C to about 95 degrees C, and wherein the thermal lysis step is carried out in a first heating zone.

47. Method according to claim 45, characterized in that it further comprises passively cooling the biological solution after the lysis step.

48. Method according to claim 45, characterized in that passively cooling the biological solution comprises flowing the biological solution through an internal passage of a cartridge, wherein the internal passage is oriented vertically,48. A method according to claim 49, characterized in that the isothermal amplification step comprises amplifying the biological solution at a temperature in a range of about 50 degrees C to about 70 degrees C, and in which the isothermal amplification step is carried out in a second heating zone.

50. A method according to claim 49, characterized in that the isothermal amplification step comprises loop-mediated isothermal amplification (LAMP).

51. A method according to claim 45, characterized in that the detectably labeled nucleic acid probe is labeled with a fluorescent marker to form a fluorescently labeled nucleic acid probe.

52. Method according to claim 51,characterized in that the fluorescently labeled nucleic acid probe comprises a fluorescent group at the 5' end of the nucleic acid probe and a quencher group at the 3' end of the nucleic acid probe.

53. Method according to claim 52, characterized in that the determination of the target nucleic acid present in the biological sample comprises: optically illuminating the biological solution; and detecting at least one fluorescent signature using at least one of a photodiode and a phototransistor, the at least one fluorescent signature being indicative of the presence of at least one target nucleic acid.

54. Method according to claim 53, characterized in that optically illuminating the biological solution comprises optically illuminating the biological solution using a light-emitting diode (LED) to emit light at a wavelength in a range of about 430 nm to about 500 nm.

55. Method according to claim 53,characterized in that the detection of at least one fluorescent signature comprises detecting at least one fluorescent signature without amplifying at least one fluorescent signature.

56. Method according to claim 45, characterized in that the target nucleic acid is eukaryotic or prokaryotic.

57. Method according to claim 56, characterized in that the target nucleic acid is protozoan, bacterial, viral or fungal.

58. Method according to claim 57, characterized in that the target nucleic acid is from Chlamydia trachomatis, Neisseria gonorrhoeae, influenza A, influenza B, SARS-CoV-2, respiratory syncytial virus (RSV) or Trichomonas vaginalis.

59. Method according to claim 53,characterized in that the detection of at least one fluorescent signature comprises passing at least one fluorescent signature through a gel filter.

60. Method for detecting the presence of at least one target nucleic acid in a biological sample, characterized in that it comprises: obtaining the biological sample from a subject, the biological sample being disposed of in a sample container; incubating the biological sample with at least one of a reagent and a buffer in the sample container, thereby producing a biological solution in the sample container; inserting the sample container into a cartridge so that the biological solution flows into an internal chamber of the cartridge,the internal chamber comprising a first heating zone; insert the cartridge into an electronic reader comprising multiple heating elements to heat the first heating zone and a second heating zone within the cartridge; perform a lysis step on the biological solution within the first heating zone; passively cool the biological solution by opening an internal passage in the cartridge so that the biological solution flows via gravity feed into the internal passage.the internal passage being fluid downstream and vertically below the internal chamber; amplifying at least one target nucleic acid in biological solution by isothermal amplification within the second heating zone comprising multiple reaction chambers fluidly downstream of the internal passage; wherein each of the multiple reaction chambers comprises: a CRISPR / Cas enzyme with collateral cleavage activity; at least one guide RNA that hybridizes specifically with at least one target nucleic acid; and a detectably labeled nucleic acid probe, wherein hybridization of the guide RNA with the target nucleic acid induces or enhances the collateral cleavage activity of the CRISPR / Cas enzyme and the CRISPR / Cas enzyme cleaves the detectably labeled nucleic acid probe.and wherein the cleavage of the detectably labeled nucleic acid probe results in an increase in detectable labeling; illuminating the biological solution within each of the multiple reaction chambers through a plurality of optical energy sources, each energy source of the plurality of optical energy sources being disposed in the vicinity of one of the multiple reaction chambers; and determining the presence of at least one nucleic acid within the biological solution based on the presence or level of the detectable marker through a detection device.

61. System for performing a nucleic acid diagnostic test, characterized in that it comprises: an electronic device capable of accepting a consumable cartridge; and the consumable cartridge configured to be installed in the electronic device and comprising reagents used in the nucleic acid diagnostic test.

62. System,According to claim 61, characterized in that the diagnostic test uses one or more reagents for the detection of a target nucleic acid sequence using CRISPR / Cas detection.

63. System, according to claim 61, characterized in that two or more separate amplification reactions occur within the consumable cartridge.

64. System, according to claim 61, characterized in that 8 amplification reactions occur within the consumable cartridge.

65. Device, according to claim 61, characterized in that fluorescence detection is used to measure molecular amplification.

66. Device, according to claim 65, characterized in that optical excitation is used to excite a sample to generate a fluorescent signal used in fluorescence detection.

67. Device, according to claim 65,characterized in that optical filtration is used to aid fluorescence detection.

68. Device according to claim 61, characterized in that thermal processing of the sample is conducted within the consumable cartridge.

69. Device according to claim 68, characterized in that thermal lysis of the sample is conducted within the consumable cartridge.

70. Device according to claim 61, characterized in that gravity is used for fluid movement within the consumable cartridge.

71. Device according to claim 61, characterized in that at least one result is displayed as a combination of: 1) illuminated indicators on the electronic device and 2) graphs on the consumable cartridge.

72. Device according to claim 61, characterized in that optical filtration is used to aid fluorescence detection.characterized in that the electronic device is configured to accept various types of consumable cartridges and to perform tests associated with each of the various types of consumable cartridges.

73. Device, according to claim 72, characterized in that the electronic device automatically detects the configuration of the consumable cartridge.

74. Device, according to claim 61, characterized in that the electronic device uses optical excitation and detection to determine whether a reaction chamber in the consumable cartridge contains a reagent.

75. Device, according to claim 74, characterized in that the determination occurs in a continuous manner.

76. Device, according to claim 74, characterized in that the determination occurs in less than 1 second.

77. Device, according to claim 61, characterized in that the electronic device automatically detects the configuration of the consumable cartridge. Petition 870250102472, dated 10 / 11 / 2025,p. 118 / 197 16 / 19 characterized by the fact that the electronic device uses optical excitation and detection to determine whether a reaction chamber in the consumable cartridge contains a liquid.

78. Device according to claim 77, characterized in that the liquid contains gas.

79. Device according to claim 77, characterized in that the liquid comprises a sample to be tested.

80. Device according to claim 77, characterized in that the determination occurs in a continuous manner.

81. Device according to claim 77, characterized in that the determination occurs in less than 1 second.

82. Device according to claim 61, characterized in that the electronic device uses optical excitation and detection to determine whether a reaction chamber contains a gas.

83. Electronic device for performing a nucleic acid diagnostic test in conjunction with a cartridge,characterized in that it comprises: a mechanical subsystem in which the cartridge is installed and positioned; an electronic subsystem that executes a test sequence based on pre-programmed parameters and unique parameters based on the type of cartridge installed; a thermal subsystem that heats two reaction zones within the cartridge; an optical subsystem that excites, filters, and detects fluorescence in real time; and a microfluidic control subsystem that actuates features in the cartridge to control the fluid flow within the cartridge.

84. Device according to claim 83, characterized in that the mechanical subsystem supports each of the electronic subsystem, the thermal subsystem, the optical subsystem, and the microfluidic control subsystem.

85. Microfluidic cartridge for performing a nucleic acid diagnostic test in conjunction with an electronic device,characterized in that it comprises: an outer coating that interacts with the electronic device when the cartridge is installed in the electronic device; reagents contained within the outer coating; a fluidic valve that is actuated by the electronic device; filter elements that allow air to pass through the outer coating and retain liquids; and a visual indication that communicates identification information related to the reagents to the electronic device through at least one of absorbance and reflectance at predetermined locations.

86. Diagnostic cartridge identification method, characterized in that it comprises: providing an apparatus for identifying a cartridge, the apparatus comprising: an optical module for measuring an optical signature within a first spectrum, wherein the optical module measures separate optical targets within the first spectrum in order to identify a cartridge type.

87. Method,According to claim 86, characterized in that the optical module is configured to measure fluorescence in a second spectrum, the second spectrum being different from the first spectrum, the second spectrum to detect the presence, within the cartridge, of at least one nucleic acid from a predetermined group of nucleic acids, the predetermined group comprising nucleic acids that are each associated with one or more indications.

88. Method, according to claim 86, characterized in that the nucleic acid comprises a human sample.

89. Method, according to claim 86, characterized in that the cartridge comprises one or more reagents for CRISPR / Cas detection.

90. Method, according to claim 86, characterized in that the cartridge comprises an identification label comprising one or more optical targets.

91. Method,91. Method according to claim 86, characterized in that the cartridge comprises at least one printed barcode label.

92. Method according to claim 86, characterized in that the optical targets comprise fluorescent ink comprising specific spectral properties.

93. Method according to claim 86, characterized in that the apparatus comprises a dual-mode photodetector configured to measure the optical signature within the first spectrum and the fluorescence within the second spectrum and two LEDs emitting light in two different spectra.

94. Method according to claim 93, characterized in that the LEDs are computer-controlled.

95. Method according to claim 91, characterized in that at least one printed barcode is printed ink (e.g., black ink, Petition 870250102472, dated 10 / 11 / 2025, page 121 / 197 19 / 19).(colored ink or combination of inks).

96. Method according to claim 93, characterized in that it further comprises: inserting the cartridge into the device; illuminating the identification label by one of the two LEDs; detecting the optical signature associated with the optical signature; and identifying the cartridge type based on the detected optical signature. Petition 870250102472, dated 10 / 11 / 2025, pp. 122 / 197,

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