WO2022251508A1

WO2022251508A1 - Reaction cartridge

Info

Publication number: WO2022251508A1
Application number: PCT/US2022/031148
Authority: WO
Inventors: Mark James Fisher; Norbert GOTTSCHLICH; Tina Roeser; Michel Neumeier
Original assignee: Proof Diagnostics
Priority date: 2021-05-28
Filing date: 2022-05-26
Publication date: 2022-12-01
Also published as: WO2022251508A9

Abstract

A fluid processing cartridge includes a sample reaction chamber with a sample inlet port and a cap configured to selectively close the sample inlet port, a waste chamber, a rehydration buffer reservoir, and a reagent chamber. A plurality of fluid flow channels include one or more fluid flow channels directly connecting the sample reaction chamber to the waste chamber, one or more fluid flow channels directly connecting the rehydration buffer reservoir to the reagent chamber, and one or more fluid flow channels directly connecting the reagent chamber to the sample reaction chamber.

Description

REACTION CARTRIDGE

FIELD OF THE DISCLOSURE

[0001] This disclosure relates to a cartridge for performing a closed reaction on a sample and obtaining a diagnostic result from the reaction.

BACKGROUND

[0002] One challenge in the area of clinical and molecular diagnostics is the ability to have a

“sample to answer” platform that requires minimal sample handling and preparation and minimal requirements for trained clinical lab personnel. Aspects of the present disclosure provide such an integrated system along with associated processes, disposable sample collection and processing components, and disposable reaction components.

SUMMARY

[0003] The following presents a simplified summary in order to provide a basic understanding of some aspects described herein. This summary is not an extensive overview of the claimed subject matter. It is intended to neither identify key or critical elements of the claimed subject matter nor delineate the scope thereof. Its sole purpose is to present some concepts in a simplified form as a prelude to the more detailed description that is presented later.

[0004] According to aspects of the disclosure, a fluid processing cartridge may include a sample reaction chamber with a sample inlet port and a cap configured to selectively close the sample inlet port, a waste chamber, a rehydration buffer reservoir containing a rehydration buffer, a reagent chamber containing a dry, rehydratable reagent, and a plurality of fluid flow channels. The fluid flow channels may include one or more fluid flow channels directly connecting the sample reaction chamber to the waste chamber, one or more fluid flow channels directly connecting the rehydration buffer reservoir to the reagent chamber, and one or more fluid flow channels directly connecting the reagent chamber to the sample reaction chamber.

[0005] According to further aspects, the one or more fluid flow channels directly connecting the rehydration buffer reservoir to the reagent chamber may include a first serpentine channel, and 1

3765885 the one or more fluid flow channels directly connecting the reagent chamber to the sample reaction chamber may include a second serpentine channel.

[0006] According to further aspects, the cap may have an opening formed therein with a pliable sealing membrane covering the opening.

[0007] According to further aspects, the fluid processing cartridge may include a base, a cover film adhered to a surface of the base, and a shell secured to a surface of the base opposite the cover film. The sample reaction chamber, the waste chamber, the rehydration buffer reservoir, the reagent chamber, and the plurality of fluid flow channels are formed between the base and the cover film, and the cap is formed in the shell.

[0008] According to further aspects, the base may include cap capture features, and the cap may include securing features configured to engage the cap capture features when the cap is closed to secure the cap in the closed position.

[0009] According to further aspects, the rehydration buffer storage reservoir further may include a fill port and a vent port.

[0010] According to further aspects, the fluid processing cartridge may further include one or more pressure ports, and the plurality of fluid flow channels may include one or more fluid flow channels connecting at least one of the one or more pressure ports to the waste chamber, the rehydration buffer reservoir, and the sample reaction chamber.

[0011] According to further aspects, the one or more pressure ports may include a first pressure port, a second pressure port, and a third pressure port, and the plurality of fluid flow channels may include one or more fluid flow channels connecting the first pressure port to the waste chamber, one or more fluid flow channels connecting the second pressure port to the rehydration buffer reservoir, and one or more fluid flow channels connecting the third pressure port to the sample reaction chamber

[0012] According to further aspects, the fluid processing cartridge may further include a first flow control element in a fluid flow passageway between the sample reaction chamber and the waste chamber, a second fluid flow control element in a fluid flow passageway between the second pressure port and the rehydration buffer reservoir, a third flow control element between the third 2

3765885 pressure port and the sample reaction chamber, a fourth flow control element in a fluid flow passageway between the rehydration buffer reservoir and the reagent chamber, and a fifth flow control element in a fluid flow passageway between the reagent chamber and the sample reaction chamber.

[0013] According to further aspects, the first pressure port, the second pressure port, and the third pressure port are configured so that a supernatant is transferred from the sample reaction chamber to the waste chamber by venting the first pressure port, closing the second pressure port, and applying positive pressure to the third pressure port, so that a rehydration buffer is transferred from the rehydration buffer reservoir to the reagent chamber, which contains a dehydrated reagent, to form the reagent mixture within the reagent chamber by closing the first pressure port, applying positive pressure to the second pressure port, and closing the third pressure port, and so that the reagent mixture is transferred from the reagent chamber to the sample reaction chamber by closing the first pressure port, applying positive pressure to the second pressure port, and venting the third pressure port.

[0014] According to further aspects, the fluid processing may include a base and a cover film adhered to a surface of the base. The sample reaction chamber, the waste chamber, the rehydration buffer reservoir, the reagent chamber, and the plurality of flow channels are formed between the base and the cover film. Each of the first, second, third, fourth, and fifth flow control elements may include a frangible seal comprising a via formed through the base and a portion of the film surrounding the via adhered to a portion of the surface of the base surrounding the via.

[0015] According to further aspects, the sample reaction chamber may include a first portion and a second portion, and the sample inlet port may be open to the first portion. The second portion is volumetrically smaller than the first portion and transverse dimensions of the second portion are smaller than transverse dimensions of the first portion, and the second portion is disposed beneath the first portion when the fluid processing cartridge is in a vertical, operative orientation.

[0016] According to further aspects, at least one wall of the second portion of the sample reaction chamber is optically transparent or translucent.

[0017] According to aspects of the disclosure, a method for performing an assay for detecting the presence or absence of an analyte of interest in a sample solution within a fluid 3

3765885 processing cartridge includes the steps of dispensing the sample solution into a sample reaction chamber of the cartridge through a sample inlet port and then closing a cap over the sample inlet port, wherein the sample solution includes magnetic target capture beads having an affinity for the analyte of interest, applying a magnetic force to an outer wall of the sample reaction chamber to draw at least a portion of the magnetic beads to an inner wall of the sample reaction chamber, transferring a supernatant from the sample reaction chamber to a waste chamber of the cartridge while applying the magnetic force to an outer wall of the sample reaction chamber to retain at least a portion of the magnetic beads in the sample reaction chamber, transferring a reagent mixture from a reagent chamber of the cartridge to the sample reaction chamber, applying heat to the contents of the sample reaction chamber, and during or after applying the heat, detecting an optical emission from the contents of the sample reaction chamber through a wall of the sample reaction chamber to determine the presence or absence of the analyte of interest in the contents of the sample reaction chamber.

[0018] According to further aspects, the method may include transferring a rehydration buffer from a rehydration buffer reservoir of the cartridge to the reagent chamber containing a dehydrated reagent to form the reagent mixture within the reagent chamber.

[0019] According to further aspects, the method may include automatically applying a visible indication to the cartridge to indicate the presence or absence of the analyte of interest.

[0020] According to further aspects, automatically applying a visible indication to the cartridge may include punching a hole in a first location on a label of the cartridge to indicate the presence of the analyte of interest or punching a hole in a second location on the label of the cartridge to indicate the absence of the analyte of interest.

[0021] According to further aspects, the method may include punching a hole in a third location on the label of the cartridge to indicate an invalid test.

[0022] According to further aspects, the fluid processing cartridge may include a first pressure port, a second pressure port, and a third pressure port. The first pressure port may be connected to the waste chamber, the second pressure port may be connected to the rehydration buffer reservoir, and the third pressure port may be connected to the sample reaction chamber. Transferring the supernatant from the sample reaction chamber to the waste chamber may include 4

3765885 venting the first pressure port, closing the second pressure port, and applying positive pressure to the third pressure port. Transferring the reagent mixture from the reagent chamber of the cartridge to the sample reaction chamber may include closing the first pressure port, applying positive pressure to the second pressure port, and venting the third pressure port.

[0023] According to further aspects, the method may include transferring a rehydration buffer from a rehydration buffer reservoir of the cartridge to the reagent chamber containing a dehydrated reagent to form the reagent mixture within the reagent chamber by closing the first pressure port, applying positive pressure to the second pressure port, and closing the third pressure port.

[0024] According to further aspects, the method may include moving the rehydration buffer back and forth through the reagent chamber by closing the first pressure port, increasing and decreasing pressure to the second pressure port; and closing the third pressure port.

[0025] According to aspects of the disclosure, a reaction cartridge may include a first pneumatic port, a second pneumatic port, and a third pneumatic port, a buffer storage reservoir, a reagent chamber containing a reagent, a waste chamber, a sample reaction chamber with a sample inlet port and a cap for closing the inlet port, a first channel connecting the third pneumatic port to the sample reaction chamber, a first fluid control valve disposed on the first channel, a second channel connecting the second pneumatic port to the buffer storage reservoir, a second fluid control valve disposed on the second channel, a third channel connecting the first pneumatic port to the waste chamber, a fourth channel connecting the buffer storage reservoir to the reagent chamber, a fourth fluid control valve disposed on the fourth channel, a fifth channel connecting the reagent chamber to the sample reaction chamber, and a fifth fluid control valve disposed on the fifth channel.

[0026] According to further aspects, the cartridge may include a label that includes results marking portions configured to be alterable by an external marking element to indicate a reaction result.

[0027] According to further aspects, the results marking portions are configured to be altered to indicate one of three different results that include invalid, positive, and negative. 5

3765885 [0028] According to further aspects, the cartridge may include a base and a housing.

[0029] According to further aspects, a wall of the sample reaction chamber is optically transparent or translucent.

[0030] According to aspects of the disclosure, a sample collection swab may include an elongated handle, optionally having an x-shaped cross section, a head disposed at an end of the handle and comprising a plurality of spaced-apart collection features comprising radially-projecting, ribs or flanges extending around the circumference of the head, and a rounded end.

[0031] According to further aspects, the ribs or flanges comprise a plurality of discrete, generally parallel flanges.

[0032] According to further aspects, the ribs or flanges comprise a single, spiral flange extending about the circumference of the head from a first end of the head to a second end of the head.

[0033] According to further aspects, the sample collection comprises a solid, unitary molded part formed from plastic.

[0034] Other features and characteristics of the subject matter of this disclosure, as well as the methods of operation, functions of related elements of structure and the combination of parts, and economies of manufacture, will become more apparent upon consideration of the following description and the appended claims with reference to the accompanying drawings, all of which form a part of this specification, wherein like reference numerals designate corresponding parts in the various figures.

BRIEF DESCRIPTION OF THE DRAWINGS

[0035] The accompanying drawings, which are incorporated herein and form part of the specification, illustrate various embodiments of the subject matter of this disclosure. In the drawings, like reference numbers indicate identical or functionally similar elements.

[0036] FIG. l is a top perspective of a reaction cartridge as disclosed herein. 6

3765885 [0037] FIG. 2 the top perspective view of the reaction cartridge, with a label removed.

[0038] FIG. 3 is a plan view of a label of the cartridge.

[0039] FIG. 4 is a partial top perspective view of a hinged cap of the cartridge.

[0040] FIG. 5 is a partial side perspective view of snapping features of the hinged cap.

[0041] FIG. 6 is a partial side perspective view of base snapping features of the cartridge.

[0042] FIG. 7 is a top perspective view of a base of the cartridge.

[0043] FIG. 8 is a top plan view of the base.

[0044] FIG. 9 is a side, exploded view of the base and cover film of the cartridge.

[0045] FIG. 10 is a bottom plan view of the base.

[0046] FIG. 11 is a cross section of the base along the line A-A in FIG.8.

[0047] FIG. 12 is a cross section of the base along the line B-B in FIG.8.

[0048] FIG. 13 is a cross section of the base along the line C-C in FIG.8.

[0049] FIGS. 14-19 are plan views of the cartridge, each showing a different step, or state, of a sample reaction process performed within the cartridge.

[0050] FIG. 20 shows a method of collecting a biological sample.

[0051] FIG. 21 is a perspective view of a capped sample collection receptacle.

[0052] FIG. 22 is a perspective view of an uncapped sample collection receptacle and showing a conical dispensing tip being attached to an open end of a vial of the receptacle.

[0053] FIG. 23 is a perspective view of sample being dispensed into a cartridge using the sample collection receptacle.

[0054] FIG. 24 is a perspective view of a cartridge being inserted into a processing device. 7

3765885 [0055] FIG. 25 is a top view of the cartridge with details showing the result marking location.

[0056] FIG. 26 is a flowchart showing a process for performing an assay on the cartridge.

[0057] FIG. 27 is a perspective view of a plug for crushing a lyophilized reagent bead within a reagent chamber of the cartridge.

[0058] FIG. 28 is a perspective view of an exemplary swab for use in the method of collecting a biological sample.

[0059] FIG. 29 is a plan view of the swab.

[0060] FIG. 30 is an end view of the swab.

[0061] FIG. 31 is a transverse cross-section of the swab.

[0062] FIG. 32 is an enlarged view of the head of the swab.

DETAILED DESCRIPTION

[0063] While aspects of the subject matter of the present disclosure may be embodied in a variety of forms, the following description and accompanying drawings are merely intended to disclose some of these forms as specific examples of the subject matter. Accordingly, the subject matter of this disclosure is not intended to be limited to the forms or embodiments so described and illustrated.

Definitions

[0064] Unless defined otherwise, all terms of art, notations and other technical terms or terminology used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this disclosure belongs. All patents, applications, published applications and other publications referred to herein are incorporated by reference in their entirety. If a definition set forth in this section is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications, and other publications that are herein incorporated by reference, the definition set forth in this section prevails over the definition that is incorporated 8

3765885 herein by reference.

[0065] Unless otherwise indicated or the context suggests otherwise, as used herein, “a” or

“an” means “at least one” or “one or more.”

[0066] This description may use various terms describing relative spatial arrangements and/or orientations or directions in describing the position and/or orientation of a component, apparatus, location, feature, or a portion thereof or direction of movement, force, or other dynamic action. Unless specifically stated, or otherwise dictated by the context of the description, such terms, including, without limitation, top, bottom, above, below, under, on top of, upper, lower, left of, right of, in front of, behind, next to, adjacent, between, horizontal, vertical, diagonal, longitudinal, transverse, radial, axial, clockwise, counter-clockwise, etc., are used for convenience in referring to such component, apparatus, location, feature, or a portion thereof or movement, force, or other dynamic action in the drawings and are not intended to be limiting.

[0067] Unless otherwise indicated, or the context suggests otherwise, terms used herein to describe a physical and/or spatial relationship between a first component, structure, or portion thereof and a second component, structure, or portion thereof, such as, attached, connected, fixed, joined, linked, coupled, or similar terms or variations of such terms, shall encompass both a direct relationship in which the first component, structure, or portion thereof is in direct contact with the second component, structure, or portion thereof and an indirect relationship in which there are one or more intervening components, structures, or portions thereof between the first component, structure, or portion thereof and the second component, structure, or portion thereof.

[0068] Unless otherwise stated, any specific dimensions mentioned in this description are merely representative of an exemplary implementation of a device embodying aspects of the disclosure and are not intended to be limiting.

[0069] To the extend used herein, terms, such as, “first,” “second,” “third,” “fourth,” etc. preceding the name of an element (e.g., a component, apparatus, location, feature, or a portion thereof or a direction of movement, force, or other dynamic action) are used for identification purposes to distinguish between similar elements, and are not intended to necessarily imply order, nor are the terms such as, “first,” “second,” “third,” “fourth,” etc. intended to preclude the inclusion of additional similar elements . 9

3765885 [0070] To the extent used herein, the term “about” applies to all numeric values and terms indicating specific physical conditions, orientations, or relationships, such as, rough, smooth, straight, horizontal, vertical, parallel, perpendicular, concentric, or similar terms, specified herein, whether or not explicitly indicated. This term generally refers to a range of numbers, conditions, orientations, and relationships that one of ordinary skill in the art would consider as a reasonable amount of deviation to the recited numeric values, conditions, orientations, and relationships (i.e., having the equivalent function or result) in the context of the present disclosure. For example, and not intended to be limiting, this term can be construed as including a deviation of ±10 percent of the given numeric value, condition, orientation, or relationship, provided such a deviation does not alter the end function or result of the stated value, condition, orientation, or relationship. Therefore, under some circumstances as would be appreciated by one of ordinary skill in the art a value of about 1% can be construed to be a range from 0.9% to 1.1%.

[0071] As used herein, the term “adjacent” refers to being near or adjoining. Adjacent objects can be spaced apart from one another or can be in actual or direct contact with one another. In some instances, adjacent objects can be coupled to one another or can be formed integrally with one another.

[0072] As used herein, the terms “substantially” and “substantial” refer to a considerable degree or extent. When used in conjunction with, for example, an event, circumstance, characteristic, or property, the terms can refer to instances in which the event, circumstance, characteristic, or property occurs precisely as well as instances in which the event, circumstance, characteristic, or property occurs to a close approximation, such as accounting for typical tolerance levels or variability of the embodiments described herein.

[0073] As used herein, the terms “optional” and “optionally” mean that the subsequently described, component, structure, element, event, circumstance, characteristic, property, etc. may or may not be included or occur and that the description includes instances where the component, structure, element, event, circumstance, characteristic, property, etc. is included or occurs and instances in which it is not or does not.

[0074] According to various embodiments, suitable reactions or processes can comprise one or more of a sample preparation process, a washing process, a sample purification process, a pre- 10

3765885 amplification process, a pre-amplified product purification process, an amplification process, an amplified product purification process, a separation process, a sequencing process, a sequencing product purification process, a labeling process, a detecting process, or the like. Processing components can comprise sample preparation components, purification components, pre amplification reaction components, amplification reaction components, sequencing reaction components, or the like. The skilled artisan can readily select and employ suitable components for a desired reaction or process, without undue experimentation.

[0075] The term “directly connected” when referring to the relationship between two different chambers or reservoirs means the chambers or reservoirs are connected to one another by a fluid flow passageway, e.g., one or more channels or conduits, with no intervening chambers or reservoirs in the fluid flow path between the two referred to chambers.

[0076] The term “indirectly connected” when referring to the relationship between two different chambers or reservoirs means the chambers or reservoirs are connected to one another by a fluid flow passageway, e.g., one or more channels or conduits, with one or more intervening chambers or reservoirs in the fluid flow path between the two referred to chambers.

Cartridge

[0077] Referring to FIGS. 1, 3, and 7, a cartridge 10 provides a point-of-care, sample-to- answer platform for performing a diagnostic test on a sample material to detect the presence or absence of an analyte of interest, such as a virus (e.g., Covid-19) or other pathogen infectious disease, genetic mark, or cancer, in the sample material. Cartridge 10 includes a base 16 with a shell, or housing, 12 fixed to the base 16 and a label 26 secured (e.g., adhesively) to a surface of the shell 12. A cover film 96 is secured to a surface of the base 16 opposite the shell 12, e.g., adhesively or by welding, see FIG. 9. Base 16 may include a plurality of grooves and depressions formed in a surface thereof, as described in further detail below, such that the film 96 secured to the surface of the base 16 encloses the depressions to form chambers and encloses the grooves to form fluid transfer channels. Base 16 may be integrally produced from plastic by injection-molding methods, for example, from polypropylene, polyethylene, cyclic olefin copolymer, polycarbonate, polymethyl methacrylate, or from a mixture of these plastics. Film 96 may be composed of the same plastics material as the base 16, although not necessarily the same material as the base to 11

3765885 which it is attached.

[0078] Shell 12 may be secured to the base 16 by means of a plurality of shell retention pins, e.g., pins 16a, 16b, 16c, 16d, 16e, and 16f, projecting from the base 16 inserted into and secured to, e.g., heat staked, a like number of retention features, e.g., blind holes 12a, 12b, 12c, 12d, 12e, and 12f formed in shell 12, see FIG. 2. Shell 12 may include a handle 14 for grasping the cartridge 10 by a user.

[0079] Cartridge 10 may include one or more registration features that are engaged by and cooperate with cooperating features within a device configured to process the cartridge 10. In one embodiment, such engagement features may comprise notches 18 formed in opposed edges of the base 16 that may be engaged by one or more spring-biased ball detents or similar mechanisms within a processing device when the cartridge 10 is inserted into a slot or other opening of the device configured to receive the cartridge, thereby positioning the cartridge 10 and releasably securing the cartridge 10 in a desired, fixed position within the device.

[0080] Referring to FIG. 3, label 26 may be pre-printed with various information-providing graphic features and/or alphanumeric indicia and/or may provide open space(s) at which information may be written or otherwise applied onto the label 26. For example, label 26 may be pre-printed at 28 with an identification of an assay, or diagnostic test, that may be performed using the cartridge 10, in the illustrated embodiment “SARS-COV-2.” Label 26 may further include a space 30 for writing or otherwise applying identifying information, such as a patient ID (which may include a patient’s name or an anonymous identifier or other identifying information for non-patient-based samples) to identify the source of the sample being tested with the cartridge 10. Label 26 may further include machine-readable indicia, such as a barcode 40. In some examples, the barcode has information relating to the cartridge 10, such as information about expiration, lot code, test type, and a unique cartridge identification number. This identification number is then used to report results and may be connected with a patient identifier in a patient database.

[0081] Label 26 may further include a result marking area 32 providing locations that may be punched or otherwise altered to indicate a test result. For example, a punch through the label, a printed mark, or other alteration at location 36 may indicate a positive test result (e.g., the presence of an analyte of interest in the sample material), at location 38 may indicate a negative test result 12

3765885 (e.g., the absence of an analyte of interest in the sample material), and at location 34 may indicate an invalid test.

[0082] Features of the base 16 are shown in FIGS. 7-13. Base 16 may include a first pneumatic port 42, a second pneumatic port 44, and a third pneumatic port 46 for cooperatively interfacing with pneumatic elements (e.g., nozzles or tubes) of a processing device. Base 16 may further include a first flow control element 48, a second flow control element 52, a third flow control element 56, a fourth flow control element 60, and a fifth flow control element 66. Each of flow control elements 48, 52, 56, 60, and 66 may comprise an alterable flow-blocking feature that is altered, e.g., melted, dissolved, punctured, delaminated, etc., by a cooperating component of the processing device to change the flow control device from a flow-blocking status to a flow- permitting status. In an embodiment, each of flow control elements 48, 52, 56, 60, and 66 comprises a frangible seal opening, or valve, that is opened by a pin of the processing device pressing on the valve to cause sufficient deflection of the material, i.e., film 96, to open the valve. In an embodiment, flow control elements 48, 52, 56, 60, and 66 may comprise a via formed through the base 16, whereby a portion of the film 96 surrounding each via separates from the base 16 when pushed by a non-puncturing pin extending through the via to permit fluid flow between the base 16 and the separated portion of the film 96.

[0083] Base 16 may further include a rehydration buffer storage reservoir 70 with a fill port

72 and a vent port 74.

[0084] One or more reagents may be provided in one or more chambers, channels, or reservoirs, such as reagent chamber 76 formed in base 16. In one embodiment, a first plug, with a dried or lyophilized reagent pellet adhered to its distal end, is inserted into an opening 78 formed in reagent chamber 76, and a second plug, with a dried or lyophilized reagent pellet adhered to its distal end, is inserted into an opening 80 formed in reagent chamber 76. The plugs may be heat- staked within the receiving openings 78, 80. Using two plugs, each with its own reagent pellet, increases the amount of rehydration buffer that can be applied to each pellet’s surface as compared to using a single plug with a larger pellet.

[0085] In another embodiment, a dried reagent (lyophilized bead) is place in the reagent chamber 76 and a plug is inserted into chamber 76 through opening 78 and/or 80 to crush the 13

3765885 reagent after it is placed in the chamber 76. FIG. 27 is a perspective view of a plug 132 for crushing a lyophilized reagent bead within a reagent chamber. Plug 132 has a body 134, which may be frustoconical in shape, with a radial flange 136 at one end and a concave crushing face 138 (i.e. the surface that contacts the dried reagent) at an opposite end. The concave face helps keep the dried reagent centered on the crushing face of the plug in the crushing process (especially for a bead form factor) and keeps the dried reagent material from jamming between the plug and the sides of openings 78, 80 while crushing. A spike 140 may be formed in the center of the concave face 138 to facilitate crushing of the bead.

[0086] In still a further embodiment, liquid reagent may be deposited in reagent chamber 76 then dried in the reagent chamber 76 prior to securing cover film 96 to the base 16.

[0087] Base 16 may further include a waste chamber 84 and a sample reaction chamber 88.

Sample reaction chamber 88 includes an upper portion 90 and a lower portion 92 when cartridge 10 is in a vertical, operative orientation as shown in FIG. 8 having a smaller volumetric capacity than the upper portion 90. Because lower portion 92 is volumetrically smaller than upper portion 90 and has smaller transverse dimensions (width and depth) than upper portion 90 (e.g., compare the relative sizes of portions 90 and 92 in FIGS. 8, 12), lower portion 92 functions as a funnel to physically concentrate the contents of chamber 88. The smaller dimensions of lower portion 92 also facilitate efficient application of magnetic forces to the contents, heating of the contents, and excitation and measurement of optical signals from the contents by efficient interfacing with thermal/magnetic components and optics components (i.e., minimize length of optical pathway) of a cartridge processing device. Lower portion 92 is a bead collection chamber as well as a reaction and detection zone and magnet and heater interface. A sample inlet 86 is open to the upper portion 90 of the sample reaction chamber 88 and includes a raised perimeter ridge 87 circumscribing the edge of the port 86.

[0088] Features of the shell 12 are shown in FIG. 2. Shell 12 may include an opening 23 through which the first, second, and third pneumatic ports 42, 44, 46 may be accessed, an opening 25 through which the flow control elements 48, 52, 56, 60, 66 may be accessed, an opening 27 through which fill port 72 and vent port 74 may be accessed, and an opening 29 through which the locations of openings 78 and 80 in reagent chamber 76 may be accessed. In an embodiment, openings 27 and 29 are covered by the label 26. Shell 12 may include results punch holes 13, 15, 14

3765885 and 17 arranged so that each of the result marking locations 34, 36, 38 of the label 26 is disposed over an associated one of the openings 13, 15, 17 to enable a hole to be punched in the portions of the label 26 over the openings 13, 15, 17.

[0089] As can be seen in FIGS. 1 and 2, at least a part of the front, or top, surface of the lower portion 92 of the sample reaction chamber 88 is not covered by shell/housing 12 so that this part of the front surface of the sample reaction chamber is exposed and accessible for contact by a magnet and/or thermal interface device.

[0090] As shown in FIGS. 2, 4, 5, and 6, shell 12 may further include a hinged cap 20 secured at one edge to a portion of the shell 12 and configured to pivot between an open position and a closed position with respect to the sample inlet port 86. Hinged cap 20 made include securing features 22a, 22b (see FIGS. 4, 5) extending laterally from an edge of the lid opposite the hinged edged that engage base capture features 24a 24b (see FIG. 6) formed in the base 16 adjacent the sample reaction chamber 88. Each of the securing features 22a and 22b may be resiliently flexible and include a detent feature that extends into the capture features 24a, 24b to secure the hinged cap 20 in a closed position. In an embodiment, cap 20 is designed to prevent inadvertent opening of the cap after it is closed, as, in certain applications, it is important that the cap is never opened particularly after amplification of the contents of reaction chamber 88. Hinged cap 20 may include an opening in which a sealing membrane 21 is secured. Sealing membrane 21 pliably contacts the raised perimeter ridge 87 surrounding the sample inlet port 86 to provide a secure seal.

[0091] Conduit grooves formed in a bottom surface of the base 16 are shown in FIG. 10.

These grooves form fluid flow channels (tubes) when the cover film 96 is applied to the bottom surface of the base 16. A first conduit 50 extends between a bottom end of lower portion 92 of sample reaction chamber 88 and waste chamber 84, passing through first flow control element 48. Thus, sample reaction chamber 88 is directly connected the to the waste chamber 84 by first conduit 50. A second conduit 54 extends between second pneumatic port 44 and fourth flow control element 60, passing through second flow control element 52 and rehydration buffer storage reservoir 70. A third conduit 58 extends between third pneumatic port 46 and a top end of upper portion 90 of sample reaction chamber 88, passing through third flow control element 56. A first serpentine conduit 62 extends between fourth flow control element 60 and reagent chamber 76. Thus, rehydration buffer storage reservoir 70 is directly connected to reagent chamber 76 by first 15

3765885 serpentine conduit 62 and a portion of second conduit 54. A second serpentine conduit 68 extends between fifth flow control element 66 and reagent chamber 76. A fourth conduit 64 extends between fifth flow control element 66 and a top end of lower portion 92 of sample reaction chamber 88. Thus, reagent chamber 76 is directly connected to sample reaction chamber 88 by second serpentine conduit 68 and fourth conduit 64. A fifth conduit 65 extends between first pneumatic port 42 and a top end of waste chamber 84. Numerical designations of components, e.g., first, second, third, etc., are for distinguishing one component from another and are not intended to be limiting or to have any implied connotation.

[0092] FIG. 26 is a flowchart showing a process 150 for performing an assay on the cartridge, and FIGS. 14-19 are plan views of the cartridge, each showing a different step, or state, of a sample reaction process performed within the cartridge.

[0093] As shown in FIGS. 14 and 26, at step SI 52, with cartridge 10 outside of a processing device, a sample solution is introduced into the sample reaction chamber 88 through the sample inlet port 86. Cartridge 10 is “pre-loaded” with a rehydration buffer in rehydration buffer storage reservoir 70 and dehydrated (e.g., lyophilized) reagent pellets or crushed beads in reagent chamber 76. The sample solution may include a sample material combined with a target capture reagent incorporating magnetic beads (e.g., nucleic acid binding bead). The bead may be coated or otherwise treated so as to have an affinity for a particular material (e.g., a target sequence) so that it can be used to capture, concentrate or otherwise enrich the particular material. The sample material may include a biological sample containing whole cells and/or live cells and/or cell debris. The biological sample may contain (or be derived from) a “bodily fluid.” Exemplary bodily fluids from which a biological sample may be obtained may include amniotic fluid, aqueous humour, vitreous humour, bile, blood serum, breast milk, cerebrospinal fluid, cerumen (earwax), chyle, chyme, endolymph, perilymph, exudates, feces, female ejaculate, gastric acid, gastric juice, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil), semen, sputum, synovial fluid, sweat, tears, urine, vaginal secretion, vomit and mixtures of one or more thereof. Biological samples include cell cultures, biopsied tissues, bodily fluids, or cell cultures from bodily fluids or biopsied tissues. Bodily fluids may be obtained from a mammal organism, for example by puncture, or other collecting or sampling procedures. Sample materials may also include non-biological samples, such as chemical samples collected from 16

3765885 industrial or municipal processing facilities.

[0094] The hinged cap 20 is then closed (as indicated by a circled “X” over sample inlet port

86 in FIG. 14), and, at step S154, the cartridge 10 is then inserted into a processing device 120 (see FIG. 24) in a vertical orientation as shown in FIG. 14 so that the sample solution collects in the lower portion 92 of the sample reaction chamber 88. While sample is being added to cartridge 10, and before the cartridge is placed in a processing device, all of the flow control elements 48, 52, 56, 60, and 66 are closed (each as represented by a circled “X” in FIG. 14) so as to prevent fluid (air or liquid) flow therethrough. For example, flow control elements 48, 56, 66 prevent sample solution from escaping the sample reaction chamber 88, and flow control elements 52, 60 prevent rehydration buffer from escaping rehydration buffer storage reservoir 70.

[0095] As shown in FIG. 15, after cartridge 10 is placed in a processing device, a lid 124

(see FIG. 24) is closed in step SI 54, and each of the flow control elements 48, 52, 56, 60, and 66 is opened, e.g., by a non-puncturing pin within the device. In an embodiment, after cartridge 10 is placed in a processing device, in step SI 56, the barcode 40 is read by a barcode reader within the processing device to confirm, e.g., (1) the presence of a cartridge in the processing device and (2) that the cartridge within the processing device has not already been processed.

[0096] An exemplary processing device is described in U.S. Provisional Patent Application

No. 63/194,659.

[0097] In step S158, a magnet/heat module (not shown) of the processing device 120 is activated - e.g., by a switch actuated when lid 124 is closed, and a heater block and magnet (not shown) of the processing device 120 are advanced to interface with portion 92 of sample reaction vessel 88. In an embodiment, a magnetic field is applied to the sample solution within the lower portion 92 of the sample reaction chamber 88 to isolate and immobilize magnetic target capture beads contained within the sample solution. In an embodiment, the magnetic field is applied by moving a magnet (not shown) into close proximity to, or contact with, the part of the front surface of the lower portion 92 of the sample reaction chamber 88 that is not covered by shell 12. The magnet draws the magnetic target capture beads out of suspension and into contact with an inner surface of lower portion 92.

[0098] As shown in FIGS. 16 and 26, in step S160, supernatant, e.g., lysis buffer, is then 17

3765885 transferred from the sample reaction chamber 88 to the waste chamber 84 via first conduit 50, and waste chamber 84 is vented via fifth conduit 65, by applying positive pressure at third pneumatic port 46, which pressure is communicated with sample reaction chamber 88 by third conduit 58, closing second pneumatic port 44, and venting first pneumatic port 42. For this purpose, first conduit 50 may be connected to a bottom end of lower portion 92 of sample reaction chamber 88 to ensure that substantially all supernatant is drained from the chamber 88, and fifth conduit 65 may be connected to a top end of waste chamber 84 to prevent waste fluid from exiting the cartridge 10 at the pneumatic port 42.

[0099] As supernatant is moved from the sample reaction chamber 88 to the waste chamber

84, immobilized target capture beads remain in the lower portion 92 of the sample reaction chamber 88, as represented at reference number 98 in FIG. 16, held to an internal wall of the lower portion 92 by the magnetic force, thereby leaving a substantially purified sample analyte in the lower portion 92 of the sample reaction chamber 88.

[00100] As shown in FIGS. 17 and 26, in step SI 62, after the supernatant is moved from the sample chamber 88 to the waste chamber 84, the dried or lyophilized reagents in reagent chamber are rehydrated, or reconstituted, by moving rehydration buffer from the rehydration buffer storage reservoir 70 to the reagent chamber 76 via first serpentine conduit 62. To achieve a thorough mixing and rehydration of the dried reagents the rehydration buffer may be moved back-and-forth through the reagent chamber 76, for which purpose the serpentine arrangements of the first serpentine conduit 62 and the second serpentine conduit 68 provide sufficient volumetric capacity. To move rehydration buffer from the rehydration buffer reservoir 70 to the reagent chamber 76, third pneumatic port 46 is closed, positive pressure is applied at second pneumatic port 44, which pressure is communicated with reservoir 70 by second conduit 54, and first pneumatic port 42 is closed. In an embodiment, to effect back-and-forth movement of the rehydration buffer through the reagent chamber 76, pneumatic ports 46 and 42 remain closed and pressure applied at second pneumatic port 44 is alternately increased and decreased.

[00101] As shown in FIGS. 18 and 26, after dried reagents are rehydrated or reconstituted, in step SI 64, the reconstituted reagent solution is moved from the reagent chamber 76 to the sample reaction chamber 88 via the second serpentine conduit 68 and the fourth conduit 64. To move the reagent solution from the reagent chamber 76 to the sample reaction chamber 88, third pneumatic 18

3765885 port 46 is vented, positive pressure is applied to second pneumatic port 44, which pressure is communicated through reservoir 70 and reagent chamber 76 and to sample reaction chamber 88 by second conduit 54, first serpentine conduit 62, second serpentine conduit 68, and fourth conduit 64, and first pneumatic port 42 is closed.

[00102] After the reagent solution is combined with the purified sample 98 within the sample reaction chamber 88, in step SI 66, the contents of the reaction chamber are exposed to reaction conditions, such as elevated temperature, which may be isothermal or thermocyclic, to incubate the contents of lower portion 92 of sample reaction chamber 88, and a reaction takes place in the lower portion 92 of sample reaction chamber 88 (e.g., a nucleic acid amplification). In one embodiment, the reaction mixture is isothermally heated to 60 deg. C.

[00103] Where an amplification procedure is used to increase the amount of target sequence present in a sample before detection can occur, it is desirable to include a “control” to ensure that amplification has taken place. Such a control can be a known nucleic acid sequence that is unrelated to the sequence(s) of interest. A probe (i.e., a control probe) having specificity for the control sequence and having a unique fluorescent dye (i.e., the control dye) is added to the sample, along with one or more amplification reagents needed to amplify the control sequence, as well as the target sequence(s). After exposing the sample to appropriate amplification conditions, the sample is alternately exposed to light energy at different excitation wavelengths (including the excitation wavelength for the control dye) and emission light is detected. Detection of emission light of a wavelength corresponding to the control dye confirms that the amplification was successful (i.e., the control sequence was indeed amplified), and thus, any failure to detect emission light corresponding to the probe(s) of the target sequence(s) is not likely due to a failed amplification. Conversely, failure to detect emission light from the control dye may be indicative of a failed amplification, thus calling into question the results from that assay.

[00104] During, or at the conclusion, of the reaction, in step SI 68, measurements of optical emissions from the reaction mixture within the lower portion 92 of the sample reaction chamber 88 may be taken, for which purpose, at least a portion of the film 96 covering the lower portion 92 is optically transparent or translucent. In an alternative embodiment, heating is applied to the film 96 side of the lower portion 92, and translucent or transparent optical window is provided in the base 16 at lower portion 92 to permit measurements of optical emissions. Obtaining measurements of 19

3765885 optical emissions from the contents of the lower portion 92 may include exposing the contents, e.g., at a location represented by reference number 130 in FIG. 19, to an optical excitation signal of a prescribed optical wavelength and measuring the magnitude or other measurable attribute of a resulting optical emission signal (e.g., a fluorescent emission) having a prescribed optical wavelength. As explained above, in some embodiments, the sample material is combined with a control material having a known response to the applied reaction conditions to ensure completion of the reaction. A detection probe reagent associated with the sample will be configured to emit an optical signal at a first optical wavelength and a detection probe reagent associated with the control material will be configured to emit an optical signal at a second optical wavelength different from the first optical wavelength.

[00105] Should an expected response (e.g., measured optical emission of the second optical wavelength measured by a control channel of an optics module (not shown) of the processing device 120 at step S170) not be obtained from the control material, an invalid test is indicated, and location 34 on label 26 may be marked at step S172 (e.g., with a visible mark and/or by punching a hole through the label at the location), thereby indicating an invalid test. Should the control signal indicate proper completion of the reaction, a positive or negative result for the tested sample will be determined by the nature of the measured response (e.g., whether an optical emission at the first optical wavelength measured from the contents of lower portion 92 reaches a predefined threshold as measured by a sample channel of an optics module at step SI 74) and the label is correspondingly marked (e.g., with a visible mark and/or by punching a hole through the label at the location) at location 36 for a positive result (step S176) or at location 38 for a negative result (step S178).

[00106] Accordingly, after sample loading onto the cartridge 10, the assay steps to be implemented on the cartridge 10 include the following:

[00107] 1. Magnetic capturing of target capture beads within the sample reaction chamber 88,

[00108] 2. Displacement of lysis buffer and transfer supernatant to the waste chamber

84,

[00109] 3. Rehydration of lyophilized reagents, e.g., crushed reagent or reagent pellets within reagent chamber 76, with rehydration buffer from the buffer reservoir 70, 20

3765885 [00110] 4. Transfer of the reconstituted reaction mixture from reagent chamber 76 to the captured beads within the sample reaction chamber 88,

[00111] 5. Heat the reaction mixture and bead pellets to 60° C, within the sample reaction chamber 88, and

[00112] 6. Read fluorescent signals (e.g. background signals, midpoint signals, and in point measurement) from the contents of sample reaction chamber 88.

[00113] Furthermore, it can be appreciated that sample collection, purification, reaction (e.g., amplification), and result detection all occur within the single, sample reaction chamber 88. In other words, the sample material is introduced to the sample reaction chamber 88 of cartridge 10 and is not thereafter moved to another chamber within the cartridge. In addition, the cartridge is physically marked at marking area 32 to provide a lasting result indication on the cartridge itself.

[00114] A sample collection system and method are illustrated in FIGS. 20, 21, and 22. In an embodiment, a biological sample may be collected, as shown in FIG. 20, by inserting a sample collection instrument 110, such as a swab having a collection tip 112, into a patient’s nasal cavity. Features of an exemplary swab are described below.

[00115] As shown in FIG. 21, a sample collection receptacle 100 includes a vial 102, with a cap 104 secured on an open and thereof, and a conical dispensing tip 106, which may be tethered to the vial 100 by a flexible tether 108. Vial 102 may contain a sample preparation solution 114, which may include reaction reagents, such as a target capture reagent and/or an amplification reagent, as well as an extraction/lysis buffer solution, such as a lysis buffer. To prepare a sample, cap 104 is removed from the vial 102, e.g., by pulling a tab 116 in the direction of the arrow. The collection tip 112 of sample collection instrument 110 is inserted into the vial 102 and submerged in the sample preparation solution 114. In some embodiments, the collection tip 112 is held in the sample preparation solution for a period of time, e.g., 30 seconds, and may be swirled to facilitate release of sample material from the collection tip 112 into the sample preparation solution 114 to form a sample reaction solution. In an embodiment, after removing the sample collection tip 112 from vial 102, cap 104 can be replaced onto the vial 102 and the capped vial can be shaken to enhance mixing of the biological material and the sample preparation solution. After removing the cap 104, the conical dispensing tip 106 is secured to the open end of the vial 102, as shown in FIG. 21

3765885 22. Next, as shown in FIG. 23, the sample collection vial 102 is inverted and the sample reaction solution is dispensed into the sample inlet port 86 of the cartridge 10. After dispensing the sample reaction mixture into the sample inlet port 86, lid 20 of the cartridge 10 is closed.

[00116] As shown in FIG. 24, a processing device 120 for processing the cartridge 10 includes a base or housing 202 and a pivoting lid 124. Cartridge 10 is inserted in the direction of the arrow into an opening 126 at the top of housing 202. Lid 124 is then closed and the sample is processed by device 120 within the cartridge 10, e.g., by performing the procedures described above in connection with FIGS. 14 - 19 and 26.

[00117] As shown in FIG. 25, a test result may be marked at result marking location 32 of a label 26 of the cartridge 10 on which sample identification information has been applied or written at location 30. The result marking may be a visible mark and/or a hole punched into the label to indicate either an invalid test result 34, a valid and negative test result 38, or a valid and positive test result 36.

[00118] Features of an exemplary swab are shown in FIGS. 28 - 32. Swab 180 includes an elongated handle 182 with a head 184 and a rounded end 186. As shown in FIGS. 28 and 30, handle 182 may have a X-shaped form factor to enhance stiffness of the handle. Swab 180 may constitute a solid, unitary molded part formed from a suitable plastic material. The enlarged head 184 is characterized by a plurality of spaced-apart collection features in the form of radially-projecting, ribs or flanges 188 extending circumferentially around the head. Exemplary dimensions of the head 184 and flange is 188 are shown in FIG. 32. Ribs or flanges 188 my comprise a plurality of discrete, generally parallel ribs or flanges, or, in an alternate embodiment, flange 188 may comprise a continuous, spiral, or helical, flange extending about the circumference of the head 184 from a first end of the head 184 (e.g., a proximal end of the head 184 where the head 184 is attached to the handle 182) to a second end of the head 184 (e.g., a distal, free end of the head 184 below the rounded end 186).

[00119] The short stiff handle 182 is specifically adapted for nasal sampling, preventing over insertion and allowing efficient sampling in the nostrils. A feature may be provided on the handle 182, such as a radially-projecting collar, to limit insertion depth of the swab within the nostril.

[00120] The closely spaced features 188 trap sample material from the nostril efficiently and 22

3765885 allow nearly all the sample material to be eluted into the sample container. In addition, the solid material of the head 184 retains much less buffer solution when the head 184 of the swab 180 is inserted into sample preparation solution 114 compared to a flocked or spun swab head. The rounded tip 186 is for patient comfort and to minimize injury if the swab is inserted too high into the nostril.

[00121] While the subject matter of this disclosure has been described and shown in considerable detail with reference to certain illustrative embodiments, including various combinations and sub-combinations of features, those skilled in the art will readily appreciate other embodiments and variations and modifications thereof as encompassed within the scope of the present disclosure. Moreover, the descriptions of such embodiments, combinations, and sub combinations is not intended to convey that the claimed subject matter requires features or combinations of features other than those expressly recited in the claims. Accordingly, the scope of this disclosure is intended to include all modifications and variations encompassed within the scope of the following appended claims. 23

3765885

Claims

1. A fluid processing cartridge comprising: a sample reaction chamber with a sample inlet port and a cap configured to selectively close the sample inlet port; a waste chamber; a rehydration buffer reservoir containing a rehydration buffer; a reagent chamber containing a dry, rehydratable reagent; and a plurality of fluid flow channels comprising one or more fluid flow channels directly connecting the sample reaction chamber to the waste chamber, one or more fluid flow channels directly connecting the rehydration buffer reservoir to the reagent chamber, and one or more fluid flow channels directly connecting the reagent chamber to the sample reaction chamber.

2 The fluid processing cartridge of claim 1, wherein the one or more fluid flow channels directly connecting the rehydration buffer reservoir to the reagent chamber comprises a first serpentine channel, and the one or more fluid flow channels directly connecting the reagent chamber to the sample reaction chamber comprises a second serpentine channel.

3 The fluid processing cartridge of claim 1, wherein the cap has an opening formed therein with a pliable sealing membrane covering the opening.

4 The fluid processing cartridge of claim 1, further comprising: a base and a cover film adhered to a surface of the base, wherein the sample reaction chamber, the waste chamber, the rehydration buffer reservoir, the reagent chamber, and the plurality of fluid flow channels are formed between the base and the cover film; and a shell secured to a surface of the base opposite the cover film, wherein the cap is formed in the shell.

5 The fluid processing cartridge of claim 4, wherein the base comprises cap capture features, and the cap comprises securing features configured to engage the cap capture features when the cap is closed to secure the cap in the closed position. 24

3765885 6 The fluid processing cartridge of claim 1, wherein the rehydration buffer storage reservoir further comprises a fill port and a vent port.

7 The fluid processing cartridge of claim 1, further comprising one or more pressure ports, wherein the plurality of fluid flow channels further include one or more fluid flow channels connecting at least one of the one or more pressure ports to the waste chamber, the rehydration buffer reservoir, and the sample reaction chamber.

8 The fluid processing cartridge of claim 7, wherein the one or more pressure ports comprise a first pressure port, a second pressure port, and a third pressure port, and wherein the plurality of fluid flow channels further include one or more fluid flow channels connecting the first pressure port to the waste chamber, one or more fluid flow channels connecting the second pressure port to the rehydration buffer reservoir, and one or more fluid flow channels connecting the third pressure port to the sample reaction chamber

9 The fluid processing cartridge of claim 8, further comprising: a first flow control element in a fluid flow passageway between the sample reaction chamber and the waste chamber; a second fluid flow control element in a fluid flow passageway between the second pressure port and the rehydration buffer reservoir; a third flow control element between the third pressure port and the sample reaction chamber; a fourth flow control element in a fluid flow passageway between the rehydration buffer reservoir and the reagent chamber; and a fifth flow control element in a fluid flow passageway between the reagent chamber and the sample reaction chamber.

10 The fluid processing cartridge of claim 8, wherein the first pressure port, the second pressure port, and the third pressure port are configured so that: a supernatant is transferred from the sample reaction chamber to the waste chamber by venting the first pressure port, closing the second pressure port; and applying positive pressure to the third pressure port, 25

3765885 a rehydration buffer is transferred from the rehydration buffer reservoir to the reagent chamber, which contains a dehydrated reagent, to form the reagent mixture within the reagent chamber by closing the first pressure port, applying positive pressure to the second pressure port, and closing the third pressure port, and the reagent mixture is transferred from the reagent chamber to the sample reaction chamber by closing the first pressure port, applying positive pressure to the second pressure port, and venting the third pressure port.

11 The fluid processing cartridge of claim 9, further comprising a base and a cover film adhered to a surface of the base, wherein the sample reaction chamber, the waste chamber, the rehydration buffer reservoir, the reagent chamber, and the plurality of flow channels are formed between the base and the cover film; and wherein each of the first, second, third, fourth, and fifth flow control elements comprises a frangible seal comprising a via formed through the base and a portion of the film surrounding the via adhered to a portion of the surface of the base surrounding the via.

12 The fluid processing cartridge of claim 1, wherein the sample reaction chamber includes a first portion and a second portion, wherein the sample inlet port is open to the first portion, wherein the second portion is volumetrically smaller than the first portion and transverse dimensions of the second portion are smaller than transverse dimensions of the first portion, and wherein the second portion is disposed beneath the first portion when the fluid processing cartridge is in a vertical, operative orientation.

13 The fluid processing cartridge of claim 12, wherein at least one wall of the second portion of the sample reaction chamber is optically transparent or translucent.

14 A method for performing an assay for detecting the presence or absence of an analyte of interest in a sample solution within a fluid processing cartridge, wherein the method comprises the steps of:

(A) dispensing the sample solution into a sample reaction chamber of the cartridge through a sample inlet port and then closing a cap over the sample inlet port, wherein the sample solution includes magnetic target capture beads having an affinity for the analyte of interest; 26

3765885 (B) applying a magnetic force to an outer wall of the sample reaction chamber to draw at least a portion of the magnetic beads to an inner wall of the sample reaction chamber;

(C) transferring a supernatant from the sample reaction chamber to a waste chamber of the cartridge while applying the magnetic force to an outer wall of the sample reaction chamber to retain at least a portion of the magnetic beads in the sample reaction chamber;

(D) after step (C), transferring a reagent mixture from a reagent chamber of the cartridge to the sample reaction chamber;

(E) after step (D), applying heat to the contents of the sample reaction chamber; and

(F) during or after step (E), detecting an optical emission from the contents of the sample reaction chamber through a wall of the sample reaction chamber to determine the presence or absence of the analyte of interest in the contents of the sample reaction chamber.

15 The method of claim 14, further comprising, prior to step (D), transferring a rehydration buffer from a rehydration buffer reservoir of the cartridge to the reagent chamber containing a dehydrated reagent to form the reagent mixture within the reagent chamber.

16 The method of claim 14, further comprising, after step (F), automatically applying a visible indication to the cartridge to indicate the presence or absence of the analyte of interest.

17 The method of claim 16, wherein automatically applying a visible indication to the cartridge comprises punching a hole in a first location on a label of the cartridge to indicate the presence of the analyte of interest or punching a hole in a second location on the label of the cartridge to indicate the absence of the analyte of interest.

18 The method of claim 17, further comprising punching a hole in a third location on the label of the cartridge to indicate an invalid test.

19 The method of claim 14, wherein the fluid processing cartridge comprises a first pressure port, a second pressure port, and a third pressure port, and wherein the first pressure port is connected to the waste chamber, the second pressure port is connected to the rehydration buffer reservoir, and the third pressure port is connected to the sample reaction chamber, and wherein: step (C) comprises venting the first pressure port, closing the second pressure port, and applying positive pressure to the third pressure port, and step (D) comprise closing the first pressure port, applying positive pressure to the second pressure port, and venting the third pressure port. 27

3765885 20 The method of claim 19, further comprising, prior to step (D), transferring a rehydration buffer from a rehydration buffer reservoir of the cartridge to the reagent chamber containing a dehydrated reagent to form the reagent mixture within the reagent chamber by closing the first pressure port, applying positive pressure to the second pressure port, and closing the third pressure port.

21 The method of claim 20, further comprising the step of moving the rehydration buffer back and forth through the reagent chamber by closing the first pressure port, alternately increasing and decreasing pressure to the second pressure port; and closing the third pressure port.

22 A reaction cartridge comprising: a first pneumatic port, a second pneumatic port, and a third pneumatic port; a buffer storage reservoir; a reagent chamber containing a reagent; a waste chamber; a sample reaction chamber with a sample inlet port and a cap for closing the inlet port; a first channel connecting the third pneumatic port to the sample reaction chamber; a first fluid control valve disposed on the first channel; a second channel connecting the second pneumatic port to the buffer storage reservoir; a second fluid control valve disposed on the second channel; a third channel connecting the first pneumatic port to the waste chamber; a fourth channel connecting the buffer storage reservoir to the reagent chamber; a fourth fluid control valve disposed on the fourth channel; a fifth channel connecting the reagent chamber to the sample reaction chamber; and a fifth fluid control valve disposed on the fifth channel.

23 The cartridge of claim 22, further comprising a label, wherein the label includes results marking portions configured to be alterable by an external marking element to indicate a reaction result.

24 The cartridge of claim 23, wherein the results marking portions are configured to be altered to indicate one of three different results comprising invalid, positive, and negative.

25 The cartridge of claim 22, further comprising a base and a housing. 28

3765885 26 The cartridge of claim 22, wherein a wall of the sample reaction chamber is optically transparent or translucent.

27 A sample collection swab comprising: an elongated handle, optionally having an x-shaped cross section; a head disposed at an end of the handle and comprising a plurality of spaced-apart collection features comprising radially-projecting, ribs or flanges extending around the circumference of the head; and a rounded end.

28 The sample collection swab of claim 27, wherein the ribs or flanges comprise a plurality of discrete, generally parallel flanges.

29 The sample collection swab of claim 27, wherein the ribs or flanges comprise a single, spiral flange extending about the circumference of the head from a first end of the head to a second end of the head.

30 The sample collection swab of claim 27, comprising a solid, unitary molded part formed from plastic. 29

3765885