WO2018126119A1

WO2018126119A1 - Aerosol capture and processing device

Info

Publication number: WO2018126119A1
Application number: PCT/US2017/068929
Authority: WO
Inventors: Luke P. Lee
Original assignee: Lee Luke P
Priority date: 2016-12-30
Filing date: 2017-12-29
Publication date: 2018-07-05

Abstract

A device is disclosed for collecting, amplifying, and analyzing an aerosolized sample containing genetic material. Internal protrusions establish a large surface area for capturing genetic material from the aerosolized sample passing through an internal sample chamber of the device. The entire device can then be placed in a thermal cycler to perform polymerase chain reaction amplification without the need to remove the sample. Primers and/or other materials can be included in the device or added after sample collection. After amplification, the entire device can be analyzed without removing the amplified genetic material from the device, such as through measured fluorescence. The device, including the internal protrusions, can be made from or include a plasmonic layer protected by a coating of thin-film (e.g., SiO₂ or Al₂O₃), which can help avoid fluorescent quenching during analysis. The entire device can quickly, easily, efficiently, and disposably analyze genetic material in an aerosolized sample.

Description

AEROSOL CAPTURE AND PROCESSING DEVICE

Cross Reference to Related Applications

[0001] The present application claims the benefit of U.S. Provisional Patent

Application No. 62/440,740 filed December 30, 2016 and entitled "AEROSOL CAPTURE AND PROCESSING DEVICE," which is hereby incorporated by reference in its entirety

Technical Field

[0002] The present disclosure relates to the sampling and analysis of biological materials generally and more specifically to collecting, amplifying, and analyzing aerosolized nucleic acids (NA) samples, such as deoxyribonucleic acid (DNA), ribonucleic acid (RNA), micro RNA (miRNA), or exosome-microRNA.

Brief Description of the Drawings

[0003] The specification makes reference to the following appended figures, in which use of like reference numerals in different figures is intended to illustrate like or analogous components. For illustrative purposes, some figures may not be drawn to scale.

[0004] FIG. 1 is schematic diagram depicting an aerosolized collection, amplification, and analysis system according to certain aspects of the present disclosure.

[0005] FIG. 2 is an isometric diagram depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0006] FIG. 3 is a partial cutaway isometric diagram depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0007] FIG. 4 is a front view depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0008] FIG. 5 is a side view depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0009] FIG. 6 is a cutaway side view taken along line B:B of FIG. 2 depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0010] FIG. 7 is a cutaway front view taken along line A:A of FIG. 2 depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0011] FIG. 8 is a schematic side view depicting a protrusion array with upper and lower protrusions extending across most of the thickness of an aerosolized sample collection device according to certain aspects of the present disclosure. [0012] FIG. 9 is a schematic side view depicting a protrusion array with protrusions extending fully across the thickness of an aerosolized sample collection device according to certain aspects of the present disclosure.

[0013] FIG. 10 is a schematic side view depicting a protrusion array with rounded, lower protrusions extending across most of the thickness of an aerosolized sample collection device according to certain aspects of the present disclosure.

[0014] FIG. 11 is a schematic side view depicting a protrusion array with pyramidal upper and lower protrusions extending across most of the thickness of an aerosolized sample collection device according to certain aspects of the present disclosure.

[0015] FIG. 12 is a cutaway top view taken along line C:C of FIG. 2 depicting an aerosolized sample collection device according to certain aspects of the present disclosure.

[0016] FIG. 13 is a top view depicting a lower protrusion according to certain aspects of the present disclosure.

[0017] FIG. 14 is a cutaway side view depicting the top portion of a lower protrusion according to certain aspects of the present disclosure.

[0018] FIG. 15 is a schematic side view depicting an analysis system for detecting radiation emitted from an aerosolized sample collection device prepared with multiple primers according to certain aspects of the present disclosure.

[0019] FIG. 16 is a flowchart depicting a process for collecting, amplifying, and analyzing a sample using an aerosolized sample collection device according to certain aspects of the present disclosure.

[0020] FIG. 17 is a schematic diagram depicting use of an aerosolized collection device according to certain aspects of the present disclosure.

[0021] FIG. 18 is a schematic diagram depicting an aerosolized collection device according to certain aspects of the present disclosure.

[0022] FIG. 19 is a schematic diagram depicting a process of collecting and amplifying NA samples using an aerosolized collection device according to certain aspects of the present disclosure.

[0023] FIG. 20 is a schematic diagram depicting processing of NA samples using an aerosolized collection device and processing device according to certain aspects of the present disclosure. [0024] FIG. 21 is a set of diagrams depicting fluid flow through a cavity of an aerosolized collection device having domes of various heights according to certain aspects of the present disclosure.

[0025] FIG. 22 is a set of charts depicting normalized particle concentration in the cavity of FIG. 22 at various inlet fluid flow velocities, depicting normalized particle concentration (C_p) as a function of time (seconds) for various dome heights according to certain aspects of the present disclosure.

[0026] FIG. 23 is a set of charts depicting residence time statistics in the cavity of

FIG. 22 depicting residence time statistics as functions of inlet fluid flow velocities for various dome heights according to certain aspects of the present disclosure.

[0027] FIG. 24 is an axonometric diagram depicting flow through a long side of an array of cavities in an aerosolized collection device according to certain aspects of the present disclosure.

[0028] FIG. 25 is a top-view flow diagram depicting flow through the array of cavities of FIG. 24 according to certain aspects of the present disclosure.

[0029] FIG. 26 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane just beyond the height of the dome according to certain aspects of the present disclosure.

[0030] FIG. 27 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane intersecting the dome according to certain aspects of the present disclosure.

[0031] FIG. 28 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane intersecting the dome and intersecting more of the dome than the plane of FIG. 27 according to certain aspects of the present disclosure.

[0032] FIG. 29 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane just beyond the height of the dome according to certain aspects of the present disclosure.

[0033] FIG. 30 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane intersecting the dome according to certain aspects of the present disclosure.

[0034] FIG. 31 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 24 taken along a plane intersecting the dome and intersecting more of the dome than the plane of FIG. 30 according to certain aspects of the present disclosure. [0035] FIG. 32 is an axonometric diagram depicting flow through a long side of an array of cavities in an aerosolized collection device according to certain aspects of the present disclosure.

[0036] FIG. 33 is a top-view flow diagram depicting flow through the array of cavities of FIG. 32 according to certain aspects of the present disclosure.

[0037] FIG. 34 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane just beyond the height of the dome according to certain aspects of the present disclosure.

[0038] FIG. 35 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane intersecting the dome according to certain aspects of the present disclosure.

[0039] FIG. 36 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane intersecting the dome and intersecting more of the dome than the plane of FIG. 35 according to certain aspects of the present disclosure.

[0040] FIG. 37 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane just beyond the height of the dome according to certain aspects of the present disclosure.

[0041] FIG. 38 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane intersecting the dome according to certain aspects of the present disclosure.

[0042] FIG. 39 is a flow diagram depicting the fluid flow through the array of cavities of FIG. 32 taken along a plane intersecting the dome and intersecting more of the dome than the plane of FIG. 38 according to certain aspects of the present disclosure.

[0043] FIG. 40 is a set of illustrations depicting central fluid flow through a cylindrical chamber of an aerosolized collection device according to certain aspects of the present disclosure.

[0044] FIG. 41 is a set of illustrations depicting cross fluid flow through a cylindrical chamber of an aerosolized collection device according to certain aspects of the present disclosure.

[0045] FIG. 42 is a set of illustrations depicting offset fluid flow through a cylindrical chamber of an aerosolized collection device according to certain aspects of the present disclosure. [0046] FIG. 43 is a set of illustrations depicting central fluid flow through a spherical chamber of an aerosolized collection device according to certain aspects of the present disclosure.

[0047] FIG. 44 is a set of illustrations depicting cross fluid flow through a spherical chamber of an aerosolized collection device according to certain aspects of the present disclosure.

[0048] FIG. 45 is a set of illustrations depicting offset fluid flow through a spherical chamber of an aerosolized collection device according to certain aspects of the present disclosure.

[0049] FIG. 46 is an axonometric flow diagram depicting fluid flow through a series of closely offset spherical chambers of an aerosolized collection device according to certain aspects of the present disclosure.

[0050] FIG. 47 is a cross-sectional flow diagram depicting fluid flow through the series of closely offset spherical chambers of FIG. 46 according to certain aspects of the present disclosure.

[0051] FIG. 48 is an axonometric flow diagram depicting fluid flow through a series of offset spherical chambers of an aerosolized collection device according to certain aspects of the present disclosure.

[0052] FIG. 49 is a cross-sectional flow diagram depicting fluid flow through the series of offset spherical chambers of FIG. 48 according to certain aspects of the present disclosure.

[0053] FIG. 50 is an axonometric flow diagram depicting fluid flow through a series of parallel-offset spherical chambers of an aerosolized collection device according to certain aspects of the present disclosure.

[0054] FIG. 51 is a cross-sectional flow diagram depicting fluid flow through the series of parallel-offset spherical chambers of FIG. 50 according to certain aspects of the present disclosure.

[0055] FIG. 52 is a schematic view and close-up view of a serialized array of chambers of an aerosolized collection device according to certain aspects of the present disclosure.

[0056] FIG. 53 is a schematic view and close-up view of an interconnected array of chambers of an aerosolized collection device according to certain aspects of the present disclosure. [0057] FIG. 54 is an axonometric diagram depicting a clamshell-style aerosolized collection device according to certain aspects of the present disclosure.

[0058] FIG. 55 is a top view depicting the bottom body of the clamshell aerosolized collection device of FIG. 54 according to certain aspects of the present disclosure.

[0059] FIG. 56 is a see-through, side view depicting the clamshell aerosolized collection device of FIG. 54 according to certain aspects of the present disclosure.

[0060] FIG. 57 is a cross-sectional side view of an aerosolized collection device according to certain aspects of the present disclosure.

Detailed Description

[0061] Certain aspects and features of the present disclosure relate to a device for collecting, amplifying, and analyzing an aerosolized sample containing genetic material, such as DNA, RNA, miRNA, or exosome-microRNA. The device can contain an array of internal protrusions designed to capture genetic material from an aerosolized sample passing through an internal sample chamber of the device. The internal protrusions are designed and arranged to provide a large surface area within the device. Once a sample has been collected, the entire device can be placed in a thermal cycler to perform polymerase chain reaction (PCR) amplification without the need to transfer the sample to another receptacle. The device can be prepared to include any desired primers and/or other materials, or such materials can be added after sample collection. In some cases, the collection device can include equipment for performing thermal cycling without a separate thermal cycler. After undergoing amplification, the entire device can be placed in an instrument for analysis, such as through measurement of fluorescence. The device, including the internal protrusions, can be made from or include a plasmonic layer protected by a coating (e.g., S1O2 or A1₂0₃), which can help avoid fluorescent quenching during analysis. The entire device can provide a quick, accurate, easy, efficient, and disposable solution for analyzing genetic material in an aerosolized sample. The device enables new, non-invasive methods for detecting NA biomarkers, for rapid and accurate identifications of pathogens, or for other molecular diagnostics of diseases or research uses.

[0062] In use, the device is able to capture aerosol samples (e.g., collected from a patient's exhaled breath condensate), amplify any NAs present in the sample using PCR amplification, and optionally detect one or more DNA analyte(s) of interest, such as using fluorescent probes. Exhaled breadth condensate (EBC) can include water vapor, water- soluble substances (e.g., around 99%), and insoluble substances (e.g., around 1%). Insoluble substances entrained in the EBC can accumulate in the collection device. The device can be hand-held in size, or any other suitable size. The device can be made from materials suitable for exposure to the thermal cycling and temperatures used for PCR amplification. For example, the device can be made using materials suitable for withstanding temperatures between at or below approximately 50° C or potentially at or below approximately 4° C, as well as at or above approximately 96° C or potentially as at or above approximately 98° C.

[0063] The sample collection device disclosed herein can be used to collect genetic material from an aerosol sample. Examples of aerosol samples can include exhaled breath or an atmosphere in an environment (e.g., a hospital room). In some cases, the device can be used to collect genetic material from any fluid sample, such as a gas-borne or liquid-borne sample. The sample collection device includes a sample chamber having an inlet and an outlet. The aerosolized sample (e.g., exhaled breath) can be provided to the inlet and can be pressurized through the sample chamber and out the outlet. The sample may be pressurized through positive pressure (e.g., force of a user exhaling into the inlet) or negative pressure (e.g., a vacuum source coupled to the outlet). In some cases, the inlet and outlet are located on opposite sides of the collection device, but they can be located in any suitable location, including on the same side of the collection device. When the inlet and outlet are located on opposite sides of the collection device, the sample chamber - and thus the collection device itself - can be dimensioned to have a length (e.g., between the inlet and outlet) that is longer than its width. In some cases, such as when the inlet and outlet are located on the same side, the sample chamber can include one or more internal walls to facilitate the aerosol sample passing through as much of the sample chamber as possible before exiting through the outlet.

[0064] The sample collection device can include an array of protrusions within the sample chamber. The protrusions can be positioned to define a tortuous path through the sample chamber. The protrusions can take any suitable form and can be designed to increase the collection device's surface area exposed to an aerosolized sample passing through the collection device. In some cases, the protrusions include upper and lower protrusions extending from the top and bottom of the sample chamber, respectively, but not completely spanning the height of the sample chamber. In some cases, the protrusions include protrusions that extend completely between the top and bottom of the sample chamber. In some cases, the protrusions are circular in shape, however they may take any suitable shape, including square, rectangular, triangular, cylindrical, spherical, cubical, pyramidal, conical, or any other suitable shape.

[0065] In some cases, the protrusions can have widths on the micrometer or millimeter scale. In some cases, the distance between adjacent protrusions can be on the micrometer to millimeter scale. The height of the protrusions can depend on the height of the sample chamber, but may be on the millimeter to centimeter scale. In some cases, any or all dimensions of the protrusions (e.g., height) and/or the protrusion array (e.g., distance between protrusions) can remain constant throughout the sample chamber. In other cases, the dimensions of the protrusions and/or the protrusion array can vary across one or more dimensions of the sample chamber.

[0066] In some cases, protrusions extend in a direction perpendicular to the direction of travel of the aerosolized sample through the sample chamber. For example, protrusions can extend between the top and bottom of the sample chamber in a direction parallel to the height of the sample chamber. However, in some cases, protrusions can extend in other directions, such as laterally between sides of the sample chamber, or at acute or oblique angles to the walls (e.g., top, bottom, or sides) of the sample chamber. In some cases, a protrusion array can be a web of interconnecting protrusions. As used herein, the term protrusion can mean an element that extends from a wall of the sample chamber, such as a side wall, a top wall, or a bottom wall. In some cases, a protrusion can extend from another protrusion. In some cases, a protrusion can include a discrete item placed in the sample chamber and adhered to or otherwise affixed to a wall of the sample chamber.

[0067] In some cases, a protrusion array can include a fixed, repeating pattern of protrusions. As one non-limiting example, a protrusion array can include adjacent, offset rows of spaced-apart protrusions. In some cases, a protrusion array can include a random or pseudo-random pattern. In some cases, the protrusion array can be engineered to establish a standing wave pattern within the sample chamber when an aerosol sample is pressurized through the sample chamber (e.g., by a user blowing). The standing wave pattern can facilitate sample collection in some cases. In some cases, the protrusion array can be engineered to disrupt any standing wave patterns within the sample chamber when an aerosol sample is pressurized through the sample chamber (e.g., by a user blowing). Disruption of standing wave patterns can facilitate sample collection in some cases.

[0068] The complexity, density, and/or arrangement of the protrusion array within the sample chamber can dictate the pressure resistance that must be overcome to successfully pass an aerosol sample through the collection device (e.g., by a user blowing through it). Collection devices can be sold and/or labeled according to this pressure resistance that is to be overcome. Thus, for each use case, an appropriate collection device can be selected. For example, a patient without strong breath support may be given a collection device with a low pressure resistance, which may require multiple sample collection attempts, whereas a patient with strong breath support may be given a collection device with a higher pressure resistance, which may require fewer sample collection attempts. In another example, a collection device used with a vacuum source can be selected to have a pressure resistance that appropriately matches the vacuum source.

[0069] The protrusions of the device, as well as any walls of the device, can be made of or can include a layer of a material suitable for reflecting, amplifying, resonating, or otherwise improving the radiation emitted within the sample chamber (e.g., by DNA probes) that is desired to be measured in an analysis step. The plasmonic layer is integrated for rapid and accurate photonic PCR, which allows LED light pulses to control for effective heat- transfer and PCR thermal cycle. For example, it is often desirable for light to be measured during an analysis step (e.g., fluorescent analysis), and thus the protrusions and walls can be made of materials designed to inhibit fluorescent quenching. The protrusions of the device, as well as any walls of the device, can be made of or can include a layer of plasmonic material. The plasmonic material can be selected from any suitable plasmonic material, including gold, aluminum, or other such plasmonic materials. In an example, the plasmonic material can be gold nanoparticles. Plasmonic materials can improve photothermal heating, enabling fast and efficient polymerized chain reactions for NA amplification.

[0070] In some cases, the protrusions of the device, as well as any walls of the device, can be further covered in a protective layer. The protective layer can be located over the plasmonic material. The protective layer can be made of any suitable material, such as Silicon Dioxide (S1O2) or Aluminum Oxide (A1₂0₃). The protective layer can help inhibit fluorescence quenching. The protective layer can be directly exposed to the aerosol sample when the aerosol sample is pressurized through the collection device.

[0071] The collection device can include a window suitable for allowing radiation to pass from the sample chamber to the analysis machine. In cases where light is being measured, the window can be an optically transparent window. In cases where other forms of radiation are being measured, the window can be transparent to the specific form of radiation being measured without necessarily being optically transparent. The window can be placed on any of the walls of the device and on more than one wall of the device. The window can occupy up to 100% of a wall of the device (e.g., one wall of the device can be made from an optically transparent material), or can occupy less than 100% of a wall of the device (e.g., the window is surrounded by a bezel of the material of the wall).

[0072] In some cases, different primers specific for different DNA sequences can be immobilized within separate regions of the sample chamber. Such a multiplexed collection device can undergo normal collection and amplification procedures and then undergo a multiplex analysis procedure, wherein the analysis machine is capable of detecting and/or measuring the presence of different DNA sequences based on measurements taken of the separate regions of the sample chamber. The separate regions need not be fluidly isolated from one another. Primers can be immobilized in the separate regions during manufacturing, immediately prior to sample collection, or prior to amplification.

[0073] In an example use case, a sample can be collected by having a patient blow into the inlet of the collection device, either directly or through a mouthpiece (e.g., a disposable and/or removable mouthpiece). DNA in the sample can be absorbed into the internal surfaces in the sample chamber and excess aerosol can exit through the outlet. The sample collection process can be performed once or repeated multiple times. In some cases, the inlet and outlet can be sealed or otherwise covered after sample collection. In some cases, the inlet and outlet can be sealed prior to sample collection, such as to maintain sterility. PCR reagents can be added to the interior of the device (e.g., prior to sealing the inlet and/or outlet or through another opening). In some cases, PCR reagents can be added to the sample chamber prior to sample collection, such as during manufacture or immediately prior to sample collection. The entire collection device can be treated according to standard PCR protocols to amplify the DNA collected in the sample chamber. The collection device can be manually processed or can be placed in an automated PCR machine (e.g., a thermal cycler). In some cases, the collection device can be placed into a custom-fit PCR machine or a custom-fit adaptor for a standard PCR machine.

[0074] After PCR amplification is complete, the entire device can be analyzed, such as through measuring fluorescence of a fluorescent probe that is specific to the nucleotide sequence of interest. In some cases, analysis can be performed manually or with an automated analysis machine. An automated analysis machine can include a sensor suitable for detecting radiation emitted from the probe in question, such as electromagnetic radiation in the form of fluorescent light. In some cases, other forms of radiation can be detected, such as nuclear radiation (e.g., from a radioactive probe), heat, visible or non-visible light, or other radiation. If desired, other measurements may be taken.

[0075] The collection device disclosed herein can be used to collect various samples, including genetic material (e.g., bare DNA), bacteria, fungi, viruses, and other materials found in an aerosolized sample (e.g., condensate from exhaled breadth or atmospheric vapor).

[0076] The collection device can be also used to amplify and detect genetic material derived from organisms found in an aerosolized sample with the use of a lysing agent to lyse the cellular membranes of those organisms. In some cases, the lysing agent can be added to the aerosolized sample prior to collection or can be introduced directly to the sample chamber, such as during manufacture, immediately prior to sample collection, during sample collection (e.g., via the same inlet or a separate inlet), or after sample collection.

[0077] These illustrative examples are given to introduce the reader to the general subject matter discussed here and are not intended to limit the scope of the disclosed concepts. The following sections describe various additional features and examples with reference to the drawings in which like numerals indicate like elements, and directional descriptions are used to describe the illustrative embodiments but, like the illustrative embodiments, should not be used to limit the present disclosure. The elements included in the illustrations herein may not be drawn to scale.

[0078] FIG. 1 is schematic diagram depicting an aerosolized collection, amplification, and analysis system 100 according to certain aspects of the present disclosure. The analysis system 100 includes a collection device 102. A user can exhale into the collection device 102, such as through a mouthpiece 106. When exhaling into the collection device 102, an aerosolized sample 104 entrained in the exhaled breath can pass into and through the collection device 102. Any excess aerosolized material 108 that is not collected by the collection device 102 can exit the collection device 102. A user can exhale into the collection device 102 one or more times.

[0079] After the aerosolized sample 104 has been collected in the collection device

102, the collection device 102 can be placed in a PCR machine 110 (e.g., a thermal cycler). Optionally, PCR reagents can be added to the sample chamber after sample collection if PCR reagents were not previously placed into the sample chamber. Within the PCR machine 110, the entire collection device 102 can be heated and cooled as necessary to perform standard PCR amplification of the genetic material collected within, without needing to remove the sample from the sample chamber. [0080] After PCR amplification is complete, the collection device 102 can be placed in or adjacent to an analysis machine 112 (e.g., a fluorescence reader). The analysis machine 112 can detect radiation 114, such as visible light. Radiation 114 (e.g., visible or non-visible light), can be emitted from DNA probes and collected by sensors of the analysis machine 112.

[0081] FIG. 2 is an isometric diagram depicting an aerosolized sample collection device 200 according to certain aspects of the present disclosure. The sample collection device 200 can be collection device 102 of FIG. 1. The collection device 200 includes a main body 216 having an inlet 218 and an outlet. The main body 216 can comprise any suitable number of walls and can take any number of suitable shapes. In some cases, the main body 216 is rectangular in shape, having a top wall, a bottom wall, and side walls. The walls can be made of or can include a plasmonic material. For example, the walls can be made of plastic with an internal layer of plasmonic material. A layer of protective material can cover the inner surfaces of the plasmonic material.

[0082] The collection device 200 includes a window 220 that allows radiation to pass between the inside of the collection device 200 and outside the collection device 200. A sample chamber inside the collection device 200 includes an array of protrusions 222. The array of protrusions 222 can increase the surface area exposed to aerosolized samples being passed into the inlet 218, through the sample chamber, and out the outlet of the collection device 200.

[0083] The collection device 200 can take any suitable shape or form and be any suitable size. However, in some cases, the collection device 200 can take a form and/or shape that approximately resembles a deck of playing cards, allowing the collection device 200 to be easily handled and manipulated by a user.

[0084] FIG. 3 is a partial cutaway isometric diagram depicting an aerosolized sample collection device 300 according to certain aspects of the present disclosure. The sample collection device 300 can be similar to the sample collection device 200 of FIG. 2. The main body 316 of the sample collection device 300 is shown in partial cutaway, depicting an array of protrusions 322 within a sample chamber 328 of the sample collection device 300. The array of protrusions 322 can take the form of a repeating pattern of protrusions 322 or may be random. The array of protrusions 322 can include protrusions extending from the top and/or the bottom of the sample chamber 328. In some cases, interior walls (not shown) can divert an aerosolized sample being pressurized through the sample chamber 328 so that the aerosolized sample contacts more surfaces within the sample chamber 328.

[0085] FIG. 4 is a front view depicting an aerosolized sample collection device 400 according to certain aspects of the present disclosure. The sample collection device 400 can be similar to the collection device 200 of FIG. 2. As seen from the front, the inlet 418 can be seen, exposing the interior of the main body 416 and the array of protrusions 422 therein. The window 420 in the illustrated example extends from the top wall of the main body 416; however in other cases the window 420 can be flush or recessed.

[0086] In some cases, the front view looks the same as a rear view, in which case the inlet 418 may look visually the same as the outlet. In some cases, the inlet 418 can take the same or a different shape or size than the outlet, or may be positioned differently than the outlet.

[0087] FIG. 5 is a side view depicting an aerosolized sample collection device 500 according to certain aspects of the present disclosure. The sample collection device 500 can be similar to the collection device 200 of FIG. 2. The window 520 in the illustrated example protrudes from the top wall of the main body 516. In some case, the opposite side view can look identical to the view in FIG. 5, although it need not.

[0088] FIG. 6 is a cutaway side view taken along line B:B of FIG. 2 depicting an aerosolized sample collection device 600 according to certain aspects of the present disclosure. The sample collection device 600 can be the same as collection device 200 of FIG. 2. The main body 616 is seen surrounding a sample chamber 626. An opening 636 is formed in a top wall of the main body 616, into which a window 620 can be secured.

[0089] The sample chamber 626 includes an array of protrusions 622, which can include lower protrusions 632 and upper protrusions 634. Lower protrusions 632 can extend upwards from the bottom wall of the main body 616, whereas upper protrusions 634 can extend downwards from the top wall of the main body 616. The lower protrusions 632 can extend upwards from the bottom wall of the main body 616 by a height 638, but remain spaced apart from the top wall of the main body 616 by a gap 642. The upper protrusions 634 can extend downwards from the top wall of the main body 616 by a height 640, but remain spaced apart from the bottom wall of the main body 616 by a gap 644. In some cases, the heights 638, 640 can extend at least approximately 50%, 55%, 60%, 65%, 70%, 75% 80%, 85%, 90% or 95% of the height within the sample chamber 626. [0090] In some cases, the main body 616 consists of a plasmonic material 628, such as gold or aluminum. In some cases, the main body 616 can by layered and can include a base outer material in addition to the plasmonic material 628. The plasmonic material 628 can be coated by a protective layer 630. The protective layer 630 can be made of any suitable material, such as, but not limited to, S1O2 or A1₂0₃.

[0091] FIG. 7 is a cutaway front view taken along line A:A of FIG. 2 depicting an aerosolized sample collection device 700 according to certain aspects of the present disclosure. The sample collection device 700 can be the collection device 200 of FIG. 2. The main body 716 is seen surrounding a sample chamber 726. An opening 736 exists in a top wall of the main body 716, into which a window 720 can be secured. The outlet 724 can be seen beyond the array of protrusions 722.

[0092] The sample chamber 726 can include an array of protrusions 722, which can include lower protrusions 732 and upper protrusions 734. Lower protrusions 732 can extend upwards from the bottom wall of the main body 716, whereas upper protrusions 734 can extend downwards from the top wall of the main body 716. The lower protrusions 732 can extend upwards from the bottom wall of the main body 716 by a height 738, but remain spaced apart from the top wall of the main body 716 by a gap 742. The upper protrusions 734 can extend downwards from the top wall of the main body 716 by a height 740, but remain spaced apart from the bottom wall of the main body 716 by a gap 744. In some cases, the heights 738, 740 can extend at least approximately 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95% of the height within the sample chamber 726.

[0093] In some cases, the main body 716 consists of a plasmonic material 728, such as gold or aluminum. In some cases, the main body 716 can by layered and can include a base outer material in addition to the plasmonic material 728. The plasmonic material 728 can be coated by a protective layer 730. The protective layer 730 can be made of any suitable material, such as, but not limited to, Si0₂ or A1₂0₃.

[0094] FIG. 8 is a schematic side view depicting a protrusion array 822 with upper and lower protrusions 834, 832 extending across most of the thickness of an aerosolized sample collection device 800 according to certain aspects of the present disclosure. The protrusion array 822 can be used in a sample collection device 800 such as collection device 102 of FIG. 1. The protrusion array 822 can include lower protrusions 832 extending from the bottom wall of the sample chamber of the sample collection device 800 and upper protrusions 834 extending from the top wall of the sample chamber of the sample collection device 800. The lower and upper protrusions 832, 834 can be cylindrical or rectangular in shape, although they may take other shapes. In some cases, the upper protrusions 834 have the same dimensions and shape as the lower protrusions 832, although they need not.

[0095] FIG. 9 is a schematic side view depicting a protrusion array 922 with protrusions 933 extending fully across the thickness of an aerosolized sample collection device 900 according to certain aspects of the present disclosure. The protrusion array 922 can be used in a sample collection device 900 such as collection device 102 of FIG. 1. The protrusions 933 can extend between the top and bottom walls of the sample chamber of the sample collection device 900. Protrusions 933 can have any suitable shape, such as cylindrical, rectangular, or other.

[0096] FIG. 10 is a schematic side view depicting a protrusion array 1022 with rounded, lower protrusions 1032 extending across most of the thickness of an aerosolized sample collection device 1000 according to certain aspects of the present disclosure. The protrusion array 1022 can be used in a sample collection device 1000 such as collection device 102 of FIG. 1. The lower protrusions 1032 can extend from the bottom wall of the sample chamber of the sample collection device 1000. The lower protrusions 1032 can have rounded ends. Lower protrusions 1032 can take any suitable form, such as cylindrical, rectangular, or other shapes. In some cases, an array of protrusions, such as protrusion array 1022, may only contain protrusions extending from the wall opposite the opening or window of the collection device. For example, if the collection device includes a window on its upper wall, the array of protrusions may include only lower protrusions.

[0097] FIG. 11 is a schematic side view depicting a protrusion array 1122 with pyramidal upper and lower protrusions 1134, 1132 extending across most of the thickness of an aerosolized sample collection device 1100 according to certain aspects of the present disclosure. The protrusion array 1122 can be used in a sample collection device 1100 such as collection device 102 of FIG. 1. The protrusion array 1122 can include lower protrusions 1132 extending from the bottom wall of the sample chamber of the sample collection device 1100 and upper protrusions 1134 extending from the top wall of the sample chamber of the sample collection device 1100. The lower and upper protrusions 1132, 1134 can be conical or pyramidal in shape, although they may take other shapes.

[0098] FIG. 12 is a cutaway top view taken along line C:C of FIG. 2 depicting an aerosolized sample collection device 1200 according to certain aspects of the present disclosure. The sample collection device 1200 can be the same as collection device 200 of FIG. 2. The main body 1216 is seen surrounding a sample chamber 1226. An inlet 1218 and an outlet 1224 provide fluid access to the sample chamber 1226.

[0099] The sample chamber 1226 includes an array of protrusions 1222, which can include lower protrusions 1232 and upper protrusions 1234. Lower protrusions 1232 extend upwards from the bottom wall of the main body 1216, whereas upper protrusions 1234 extend downwards from the top wall of the main body 1216.

[0100] In some cases, the main body 1216 consists of a plasmonic material 1228, such as, but not limited to, gold or aluminum. In some cases, the main body 1216 can by layered and can include a base outer material in addition to the plasmonic material 1228. The plasmonic material 1228 can be coated by a protective layer 1230. The protective layer 1230 can be made of any suitable material, such as, but not limited to, S1O2 or A1₂0₃.

[0101] The array of protrusions 1222 can include repeated patterns of protrusions, such as the lattice pattern depicted in FIG. 12. In some cases, other patterns can be used, or the array of protrusions 1222 can include a random or pseudo-random arrangement of protrusions.

[0102] FIG. 13 is a top view depicting a lower protrusion 1332 according to certain aspects of the present disclosure. The lower protrusion 1332 can be the same as lower protrusion 632 of FIG. 6. The lower protrusion 1332 can include a core 1348 surrounded by a protective layer 1346. The protective layer 1346 can be the same as protective layer 646 of FIG. 6, such as, but not limited to, Si0₂ or A1₂0₃. The core 1348 can be made from the same material as the main body or walls of the sample chamber, such as a plasmonic material. In some cases, the core 1348 is an extension of the plasmonic material of the main body of a collection device. In some cases, the protective layer 1346 is an extension of the protective layer of the main body of a collection device. While FIG. 13 depicts a lower protrusion 1332, any protrusion, such as an upper protrusion or a protrusion extending across the thickness of the sample chamber, may be similarly constructed.

[0103] FIG. 14 is a cutaway side view depicting the top portion of a lower protrusion

1432 according to certain aspects of the present disclosure. The lower protrusion 1432 can be the same lower protrusion 1332 of FIG. 13. The cutaway view shows the protective layer 1446 surrounding the core 1448.

[0104] FIG. 15 is a schematic side view depicting an analysis system 1500 for detecting radiation emitted from an aerosolized sample collection device 1502 prepared with multiple primers according to certain aspects of the present disclosure. The sample collection device 1502 can include any number of primers located within the sample chamber of the main body 1516. As depicted in FIG. 15, three primers, Primer A, Primer B, and Primer C, are located within first, second, and third regions 1550, 1552, 1554, respectively.

[0105] During analysis, as the primers in each of the first, second, and third regions

1550, 1552, 1554 fluoresce, the fluorescence reader 1512 detects the light emitted from the primers. Because regions 1550, 1552, 1554 are spatially isolated from one another (e.g., longitudinally offset along the length of the collection device 1502), each can fluoresce first, second, and third light 1556, 1558, 1560, respectively. The fluorescence reader 1512 is thus able to distinctly identify the first light 1556 attributable to the region 1550 associated with Primer A, the second light 1558 attributable to the region 1552 associated with Primer B, and the third light 1560 attributable to the region 1554 associated with Primer C. The fluorescence reader 1512 can include suitable sensors for distinguishing the presence and/or amount of light across its longitudinal length and thus is able to individually distinguish first light 1556, second light 1558, and third light 1560.

[0106] In some cases, opaque (e.g., optically opaque) blockers (not shown) can be used to limit the amount of light 1556 emitted from region 1550 from spilling into the portion of the fluorescence reader 1512 aligned with region 1552.

[0107] FIG. 16 is a flowchart depicting a process 1600 for collecting, amplifying, and analyzing a sample using an aerosolized sample collection device according to certain aspects of the present disclosure. At block 1602, the collection device is prepared. Preparing the collection device can include removing seals from the inlet and outlet of the collection device. In some cases, preparing the collection device can include putting materials, such as DNA primers, PCA reagents, lysing materials, or other materials, into the collection device.

[0108] At block 1604, the aerosol sample is collected. The aerosol sample can be collected by pressurizing an aerosol sample through the collection device, for example by exhaling into the collection device. In some cases, the aerosol sample can be collected by using negative pressure to draw an aerosol sample through the collection device. The inlet and the outlet can be sealed.

[0109] At optional block 1606, PCR reagents are placed into the sample chamber if the sample chamber does not yet have PCR reagents. In such cases, one or more of the inlet or the outlet may be left unsealed after block 1604 for insertion of the PCR reagents. In some case, other materials, such as lysing agents, can be added during block 1606. After adding the PCR reagents, the inlet and outlet of the collection device can be sealed. [0110] At block 1608, the entire sample chamber is placed in a PCR machine to undergo PCR amplification. In the PCR machine, the entire sample chamber can be subjected to thermal cycling to induce the various steps of PCR amplification. PCR amplification can thus be performed without the need to remove the sample from the collection device.

[0111] At block 1610, the sample in the collection device is analyzed. The sample can be analyzed by placing the collection device in an analysis machine, such as a machine including fluorescence sensors (e.g., optical sensors). In some cases, the collection device can be placed directly into the analysis machine. The light can be emitted through an opening in the collection device, such as through a window.

[0112] In some cases, instead of a window, the collection device can include a removable covering over the opening. In such cases, at block 1610, the removable covering can be removed to expose the sample chamber to the analysis machine.

[0113] FIG. 17 is a schematic diagram 1700 depicting use of an aerosolized collection device 1708 according to certain aspects of the present disclosure. A user 1702 can exhale particles 1704 into the collection device 1708 as exhaled breath condensate 1706. Particles 1704 entrained within the exhaled breath condensate 1706 can become trapped within the collection device 1708, such as within cavities 1710 of the collection device 1708. As depicted in FIG. 17, an enlarged view of a cavity 1710 (e.g., a chamber) shows fluid flow patterns within the cavity 1710 and captured particles 1712 that are collected by the collection device 1708.

[0114] FIG. 18 is a schematic diagram 1800 depicting an aerosolized collection device 1802 according to certain aspects of the present disclosure. The aerosolized collection device 1802 can include an inlet 1804 and an outlet 1806 fluidly coupled within the collection device 1802 to allow passage of fluid through a cavity array 1808. The cavity array 1808 can include multiple cavities 1810 having an internal surface area in fluid communication with the inlet 1804 and outlet 1806. The internal surfaces of the cavities 1810 can be coated with or otherwise include surface particles designed to capture NA samples. For example, internal surfaces of the cavities 1810 can be coated with gold nanoparticles (AuNP). Coating the internal surfaces of the cavities 1810 can include depositing gold nanoparticles on the internal surfaces. In some cases, a cavity array 1808 can include 72 cavities 1810, although any suitable number of cavities 1810 can be used. [0115] Cavities 1810 can have various shapes and be fluidly coupled to the inlet 1804 and outlet 1806 in various configurations. In some cases, the cavities 1810 can be spherical in shape and connected together via passageways. In an example, as shown in cutout 1816, a cavity 1810 can include a generally spherical shape with an internal dome-shaped surface 1818. The dome-shaped surface can be generally shaped as a sphere segment or a spherical cap. A pair of passageways 1820 can fluidly couple the cavity 1810 in a plane offset from the center of the cavity 1810. Cutout 1818 depicts front, side, and top views of the cavity 1810.

[0116] In some cases, the aerosolized collection device 1802 can be made form a transparent or translucent material, such as acrylic glass (e.g., Polymethyl methacrylate (PMMC)). An energy source 1812, such as a light source (e.g., light emitting diode (LED)), can be positioned adjacent the collection device 1802 and positioned to provide energy to the cavity array 1808. The energy source 1812 can provide energy to perform thermal cycling or be used for probe detection of the collection device 1802. In some cases, the energy source 1812 can be coupled to or part of the collection device 1802, or can be incorporated into a separate device (e.g., a thermal cycler).

[0117] FIG. 19 is a schematic diagram depicting a process 1900 of collecting and amplifying NA samples using an aerosolized collection device according to certain aspects of the present disclosure. NA samples 1904 can become captured in a cavity 1902 of the collection device in a capture phase. In a heating phase, thermal energy can be provided to the cavity 1902, such as through light 1906 emitted by a light source (e.g., one or more LEDs). Thermal energy providing in the heating phase can denature NA samples 1904. In a cooling phase, application of thermal energy can cease (e.g., by turning off the light source), allowing the NA samples 1904 in the cavity 1902 to undergo annealing and elongation (e.g., extension). Heating and cooling phases can be repeated as necessary to achieve a desired amount of NA sample replication. In some cases, additional heating phases can be achieved by powering the light source under different duty cycles to provide desired amounts of thermal energy.

[0118] FIG. 20 is a schematic diagram 2000 depicting processing of NA samples using an aerosolized collection device 2002 and processing device 2004 according to certain aspects of the present disclosure. The processing device 2004 can be a standalone device or a device couplable to a computing device 2006. In some cases, processing device 2004 can be a mobile processing device capable of coupling to a smartphone, tablet, or portable computer. In some cases, processing device 2004 can obtain power from and exchange data with the computing device 2006. The processing device 2004 can contain necessary electronics, sensors, and outputs to perform one or more processing steps associated with the aerosolized collection device 2002. In some cases, the processing device 2004 can perform one or both of PCR and data collection (e.g., NA probe detection). Processing device 2004 can include a light source or other thermal source for providing thermal energy to the collection device 2002. Processing device 2004 can include one or more sensors for measuring or inferring a temperature of the collection device 2002 to provide control of PCR steps. Processing device 2004 can include light sources suitable for fluorescing NA probes and/or sensors suitable for detecting NA probe fluorescence, such as light sensors or cameras. In some cases, the processing device 2004 can make use of sensors or energy sources of the computing device 2006. For example, a processing device 2004 can include apertures, mirrors, lenses, and/or light pipes to allow a camera or an energy source of the computing device 2006 to interact with the collection device 2002.

[0119] In use, a collection device 2002 can be inserted into a processing device 2004, which is then coupled to a computing device 2006. Processing device 2004 can be coupled to computing device 2006 through a wired connection (e.g., plug-in connection) or wireless connection (e.g., WiFi, Bluetooth, or other wireless standards). An application 2008 running on the computing device 2006 can control the processing device 2004 to perform PCR steps, collect data, or perform other functions.

[0120] FIG. 21 is a set of diagrams 2100 depicting fluid flow through a cavity 2102 of an aerosolized collection device having domes 2104 of various heights according to certain aspects of the present disclosure. To facilitate interpreting the fluid flow diagram, regions of high flow rate are depicted by dark flow lines overlaid with dark arrows. Cavities 2102 of an aerosolized collection device can include a dome 2104 designed to divert fluid flow entering the cavity 2102 into the body of the cavity 2102 before exiting the cavity 2102. Thus, particles (e.g., NA samples) entrained in the fluid flow can impact the walls of the cavity 1202 and circulate within the cavity 2102 to increase particle collection. The set of diagrams 2100 depict velocity streamlines and particle tracings (e.g., after 0.25 seconds) within a cross section of the cavity 2102 at a centerline of the cavity 2102 for various dome 2104 (e.g., hump) heights ranging from 0 mm to 0.3 mm when an inlet fluid flow velocity is 2 m/s and at a cavity diameter of approximately 1 mm. It has been determined that dome 2104 heights of approximately 0.20 mm or 0.25 mm perform well, with high concentrations of capture particles. Other values of velocity, cavity 2102 size, and dome 2104 height can be used. As seen in the set of diagrams 2100, velocity profile and streamline are altered by a dome 2104. Relatively greater recirculation can be generated within a cavity 2102 when a dome 2104 is used, than when a dome 2104 is not used (e.g., dome 2104 height = 0 mm), which can result in more particles remaining within the cavity 2102 after a given time.

[0121] FIG. 22 is a set of charts 2200 depicting normalized particle concentration in the cavity 2102 of FIG. 22 at various inlet fluid flow velocities, depicting normalized particle concentration (C_p) as a function of time (seconds) for various dome 2104 heights according to certain aspects of the present disclosure.

[0122] FIG. 23 is a set of charts 2300 depicting residence time statistics in the cavity

2102 of FIG. 22 depicting residence time statistics as functions of inlet fluid flow velocities for various dome 2104 heights according to certain aspects of the present disclosure. Chart 2302 depicts dimensionless mean residence time as a function of inlet fluid flow velocity. Chart 2304 depicts variance of the dimensionless mean residence time as a function of inlet fluid flow velocity. Chart 2306 depicts skewness of the dimensionless mean residence time as a function of inlet fluid flow velocity.

[0123] FIG. 24 is an axonometric diagram depicting flow 2402 through a long side of an array of cavities 2404 in an aerosolized collection device 2400 according to certain aspects of the present disclosure. The array of cavities 2404 is depicted in cross section, showing domes 2406.

[0124] FIG. 25 is a top-view flow diagram depicting flow through the array of cavities 2404 of FIG. 24 according to certain aspects of the present disclosure. As seen in FIG. 25, high rates of fluid flow are seen over domes 2402 and passing between adjacent cavities. To facilitate interpreting the fluid flow diagram of FIGs. 25-38, regions of high flow rate are depicted by dark flow lines overlaid with dark arrows.

[0125] FIG. 26 is a flow diagram depicting the fluid flow through the array of cavities

2404 of FIG. 24 taken along a plane just beyond the height of the dome 2402 according to certain aspects of the present disclosure.

[0126] FIG. 27 is a flow diagram depicting the fluid flow through the array of cavities

2404 of FIG. 24 taken along a plane intersecting the dome 2402 according to certain aspects of the present disclosure. [0127] FIG. 28 is a flow diagram depicting the fluid flow through the array of cavities

2404 of FIG. 24 taken along a plane intersecting the dome 2402 and intersecting more of the dome 2402 than the plane of FIG. 27 according to certain aspects of the present disclosure.

[0128] FIG. 29 is a flow diagram depicting the fluid flow through the array of cavities

[0129] FIG. 30 is a flow diagram depicting the fluid flow through the array of cavities

2404 of FIG. 24 taken along a plane intersecting the dome 2402 according to certain aspects of the present disclosure.

[0130] FIG. 31 is a flow diagram depicting the fluid flow through the array of cavities

2404 of FIG. 24 taken along a plane intersecting the dome 2402 and intersecting more of the dome 2402 than the plane of FIG. 30 according to certain aspects of the present disclosure.

[0131] FIG. 32 is an axonometric diagram depicting flow 3202 through a long side of an array of cavities 3204 in an aerosolized collection device 3200 according to certain aspects of the present disclosure. The array of cavities 3204 is depicted in cross section, showing domes 3206.

[0132] FIG. 33 is a top-view flow diagram depicting flow through the array of cavities 3204 of FIG. 32 according to certain aspects of the present disclosure. As seen in FIG. 33, high rates of fluid flow are seen over domes 3202 and passing between adjacent cavities. To facilitate interpreting the fluid flow diagram, regions of high flow rate are depicted by dark flow lines overlaid with dark arrows.

[0133] FIG. 34 is a flow diagram depicting the fluid flow through the array of cavities

3204 of FIG. 32 taken along a plane just beyond the height of the dome 3202 according to certain aspects of the present disclosure.

[0134] FIG. 35 is a flow diagram depicting the fluid flow through the array of cavities

3204 of FIG. 32 taken along a plane intersecting the dome 3202 according to certain aspects of the present disclosure. To facilitate interpreting the fluid flow diagram, regions of high flow rate are depicted by dark flow lines overlaid with dark arrows.

[0135] FIG. 36 is a flow diagram depicting the fluid flow through the array of cavities

3204 of FIG. 32 taken along a plane intersecting the dome 3202 and intersecting more of the dome 3202 than the plane of FIG. 35 according to certain aspects of the present disclosure. [0136] FIG. 37 is a flow diagram depicting the fluid flow through the array of cavities

[0137] FIG. 38 is a flow diagram depicting the fluid flow through the array of cavities

3204 of FIG. 32 taken along a plane intersecting the dome 3202 according to certain aspects of the present disclosure.

[0138] FIG. 39 is a flow diagram depicting the fluid flow through the array of cavities

3204 of FIG. 32 taken along a plane intersecting the dome 3202 and intersecting more of the dome 3202 than the plane of FIG. 38 according to certain aspects of the present disclosure.

[0139] FIG. 40 is a set of illustrations 4000 depicting central fluid flow through a cylindrical chamber 4002 of an aerosolized collection device according to certain aspects of the present disclosure. To facilitate interpreting the fluid flow diagram in FIGs. 40-53, regions of high flow rate are depicted by dark flow lines overlaid with dark arrows. The cylindrical chamber 4002 can include an inlet passageway 4004 and an outlet passageway 4006 located at opposite faces of the cylindrical chamber 4002. The inlet passageway 4004 and outlet passageway 4006 can both be aligned collinear with a center axis of the cylindrical chamber 4002. The cylindrical chamber 4002 can have a diameter 4008. The inlet passageway 4004 and outlet passageway 4006 can each have a diameter 4010, although they may have different diameters. In some cases, a single cylindrical chamber 4002 can include more than one inlet passageways 4004 and/or more than one outlet passageways 4006. Central flow can include fluid flowing in the cylindrical chamber 4000 in a direction substantially parallel and/or collinear to the center axis of the cylindrical chamber 4000.

[0140] The set of illustrations 4000 further depict fluid flow patterns through the cylindrical chamber 4002 at various fluid flow velocities (Vin). More mixing and recirculation within the cylindrical chamber 4002 is seen at fluid flow velocities around 1 or 2 m/s.

[0141] FIG. 41 is a set of illustrations 4100 depicting cross fluid flow through a cylindrical chamber 4102 of an aerosolized collection device according to certain aspects of the present disclosure. The cylindrical chamber 4102 can include an inlet passageway 4104 and an outlet passageway 4106 located at opposite faces of the cylindrical chamber 4102. The inlet passageway 4104 and outlet passageway 4106 can be non-collinear with one another and non-collinear with a center axis of the cylindrical chamber 4102. The inlet passageway 4104 and outlet passageway 4106 can be lie along imaginary lines located opposite the center axis of the cylindrical chamber 4102 from one another. In some cases, a single cylindrical chamber 4102 can include more than one inlet passageways 4104 and/or more than one outlet passageways 4106. Cross fluid flow can include fluid flowing into and out of a central plane that is collinear with the center axis of the cylindrical chamber 4102.

[0142] The set of illustrations 4100 further depict fluid flow patterns through the cylindrical chamber 4102 at various fluid flow velocities (Vin).

[0143] FIG. 42 is a set of illustrations 4200 depicting offset fluid flow through a cylindrical chamber 4202 of an aerosolized collection device according to certain aspects of the present disclosure. The cylindrical chamber 4202 can include an inlet passageway 4204 and an outlet passageway 4206 located at opposite faces of the cylindrical chamber 4202. The inlet passageway 4204 and outlet passageway 4206 can be collinear with one another and non-collinear with a center axis of the cylindrical chamber 4202. In some cases, the shared axis of the inlet passageway 4204 and outlet passageway 4206 can be parallel to and offset from the center axis of the cylindrical chamber 4202. In some cases, a single cylindrical chamber 4202 can include more than one inlet passageways 4204 and/or more than one outlet passageways 4206. Offset fluid flow can include fluid flowing in a direction substantially parallel to, but offset from, the center axis of the cylindrical chamber 4202.

[0144] The set of illustrations 4200 further depict fluid flow patterns through the cylindrical chamber 4202 at various fluid flow velocities (Vin).

[0145] FIG. 43 is a set of illustrations 4300 depicting central fluid flow through a spherical chamber 4302 of an aerosolized collection device according to certain aspects of the present disclosure. The spherical chamber 4302 can include an inlet passageway 4304 and an outlet passageway 4306 located at opposite ends of the spherical chamber 4302. The inlet passageway 4304 and outlet passageway 4306 can both be aligned collinear with a center axis between the ends of the spherical chamber 4302. The spherical chamber 4302 can have a diameter 4308. The inlet passageway 4304 and outlet passageway 4306 can each have a diameter 4310, although they may have different diameters. In some cases, a single spherical chamber 4302 can include more than one inlet passageways 4304 and/or more than one outlet passageways 4306. Central flow can include fluid flowing in the spherical chamber 4300 in a direction substantially parallel and/or collinear to the center axis of the spherical chamber 4300. [0146] The set of illustrations 4300 further depict fluid flow patterns through the spherical chamber 4302 at various fluid flow velocities (V_m). More mixing and recirculation within the spherical chamber 4302 is seen at fluid flow velocities around 1 or 2 m/s.

[0147] FIG. 44 is a set of illustrations 4400 depicting cross fluid flow through a spherical chamber 4402 of an aerosolized collection device according to certain aspects of the present disclosure. The spherical chamber 4402 can include an inlet passageway 4404 and an outlet passageway 4406 located at opposite ends of the spherical chamber 4402. The inlet passageway 4404 and outlet passageway 4406 can be non-collinear with one another and non-collinear with a center axis between the ends of the spherical chamber 4402. The inlet passageway 4404 and outlet passageway 4406 can be lie along imaginary lines located opposite the center axis of the spherical chamber 4402 from one another. In some cases, a single spherical chamber 4402 can include more than one inlet passageways 4404 and/or more than one outlet passageways 4406. Cross fluid flow can include fluid flowing into and out of a central plane that is collinear with the center axis of the spherical chamber 4402.

[0148] The set of illustrations 4400 further depict fluid flow patterns through the spherical chamber 4402 at various fluid flow velocities (Vm).

[0149] FIG. 45 is a set of illustrations 4500 depicting offset fluid flow through a spherical chamber 4502 of an aerosolized collection device according to certain aspects of the present disclosure. The spherical chamber 4502 can include an inlet passageway 4504 and an outlet passageway 4506 located at opposite ends of the spherical chamber 4502. The inlet passageway 4504 and outlet passageway 4506 can be collinear with one another and non- collinear with a center axis between the ends of the spherical chamber 4502. In some cases, the shared axis of the inlet passageway 4504 and outlet passageway 4506 can be parallel to and offset from the center axis of the spherical chamber 4502. In some cases, a single spherical chamber 4502 can include more than one inlet passageways 4504 and/or more than one outlet passageways 4506. Offset fluid flow can include fluid flowing in a direction substantially parallel to, but offset from, the center axis of the spherical chamber 4502.

[0150] The set of illustrations 4500 further depict fluid flow patterns through the spherical chamber 4502 at various fluid flow velocities (Vm).

[0151] FIG. 46 is an axonometric flow diagram 4600 depicting fluid flow through a series of closely offset spherical chambers 4602 of an aerosolized collection device according to certain aspects of the present disclosure. The spherical chambers 4602 can be arranged serially, such that an outlet passageway of one spherical chamber 4602 is the inlet passageway of a subsequent spherical chamber 4602. In some cases, a collection device can include one or more collections of serial chambers fluidly coupling the inlet of the collection device with the outlet of the collection device.

[0152] FIG. 47 is a cross-sectional flow diagram 4700 depicting fluid flow through the series of closely offset spherical chambers 4602 of FIG. 46 according to certain aspects of the present disclosure. In some cases, the chambers 4602 can be arranged to produce a dimensionless residence time that is at or approximately 202.61.

[0153] FIG. 48 is an axonometric flow diagram 4800 depicting fluid flow through a series of offset spherical chambers 4802 of an aerosolized collection device according to certain aspects of the present disclosure. The spherical chambers 4802 can be arranged serially, such that an outlet passageway of one spherical chamber 4802 is the inlet passageway of a subsequent spherical chamber 4802. In some cases, a collection device can include one or more collections of serial chambers fluidly coupling the inlet of the collection device with the outlet of the collection device.

[0154] FIG. 49 is a cross-sectional flow diagram 4900 depicting fluid flow through the series of offset spherical chambers 4802 of FIG. 48 according to certain aspects of the present disclosure. In some cases, the chambers 4802 can be arranged to produce a dimensionless residence time that is at or approximately 199.34. Comparison of FIGs. 47 and 49 show that a higher dimensionless residence time can be achieved by decreasing the serial distance between subsequent chambers.

[0155] FIG. 50 is an axonometric flow diagram depicting fluid flow through a series of parallel-offset spherical chambers 5002 of an aerosolized collection device according to certain aspects of the present disclosure. The parallel-offset spherical chambers 5002 can be arranged in parallel groups, each group serially arranged with subsequent groups. Multiple (e.g., two) spherical chambers 5002 of a parallel group can share a single inlet passageway. One or more outlet passageways of a parallel group can then feed into the inlet passageway of a subsequent parallel group. In some cases, a collection device can include one or more collections of serial parallel groups of chambers fluidly coupling the inlet of the collection device with the outlet of the collection device.

[0156] FIG. 51 is a cross-sectional flow diagram 5100 depicting fluid flow through the series of parallel-offset spherical chambers 5002 of FIG. 50 according to certain aspects of the present disclosure. In some cases, the chambers 5002 can be arranged to produce a dimensionless residence time that is at or approximately 209.13. Comparison of FIGs. 47 and 51 show that a higher dimensionless residence time can be achieved by arranging the chambers in parallel groups.

[0157] FIG. 52 is a schematic view and close-up view of a serialized array of chambers 5200 of an aerosolized collection device according to certain aspects of the present disclosure. The array 5200 can include one or more serial paths 5202, each path 5202 containing a set of chambers 5204 (e.g., spherical chambers) arranged in serial between the inlet and outlet of the aerosolized collection device.

[0158] FIG. 53 is a schematic view and close-up view of an interconnected array of chambers 5300 of an aerosolized collection device according to certain aspects of the present disclosure. The array 5300 can include multiple chambers 5204 arranged between the inlet and outlet of the aerosolized collection device. The array 5300 may be interconnected because some or all chambers 5204 are interconnected with neighboring chambers 5204 serially and in parallel.

[0159] FIG. 54 is an axonometric diagram depicting a clamshell-style aerosolized collection device 5400 according to certain aspects of the present disclosure. The collection device 5400 can include features formed into a top body 5404 and a bottom body 5406 such that chambers 5402 are formed when the top body 5404 is placed against the bottom body 5406.

[0160] FIG. 55 is a top view depicting the bottom body 5406 of the clamshell aerosolized collection device 5400 of FIG. 54 according to certain aspects of the present disclosure. The bottom body 5406 is depicted having an inlet portion of 20 mm in length and an array portion of 48 mm in length and 25 mm in width. Other sizes may be used.

[0161] FIG. 56 is a see-through, side view depicting the clamshell aerosolized collection device 5400 of FIG. 54 according to certain aspects of the present disclosure. The height of the collection device 5400 is shown as being 2 mm. The diameter of each chamber 5402 is shown as being 1 mm. The width of the inlet portion is shown as being 10 mm. Other sizes may be used.

[0162] FIG. 57 is a sectional side view of an aerosolized collection device 5700 according to certain aspects of the present disclosure. The aerosolized collection device 5700 includes multiple chambers 5702 formed between a top body portion 5704 and a bottom body portion 5706. The top body portion 5704 and bottom body portion 5706 can be of unibody construction or made of multiple parts. In some cases, the aerosolized collection device 5700 can be shaped to be mirrored across one or more axes of the aerosolized collection device 5700 such that the aerosolized collection device 5700 can be inserted into a processing device in any multiple different direction (e.g., in a first direction or in a second direction opposite the first direction).

[0163] Fluid dynamic simulations were performed on various styles of collection devices, such as those described herein with reference to the various figures. In certain simulations, air flow in a channel was assumed as incompressible laminar flow (Reynolds number (Re) = 186 to 960 for v,„ = 1 to 4 m/s). Particle tracing was also performed based on the computed velocity field by assuming NAs as particles having a diameter of d_p = 2 nm and a mass of m_p = 3.59e^~12 g. Simulations included releasing 1,000 particles at the inlet at t = 0.1 s. The particle motions were derived by the net force (FN) acting on the particles which is a resultant force of the drag force (FD) and Brownian force (FB). Here, Reynolds number is determined by Re = ^pv™^De _? where p and μ are density (1.225 kg/m³) and viscosity (1.95e^~5

Pa-s) of air, respectively. Vm is inlet velocity. D_e is equivalent diameter (D_e = 130(a-b)^{0 625} 1 {a + b)^{0 25}; a = 10 mm and b = 1 mm of mouthpiece). Inter-particle interaction was neglected due to low concentration of molecules in breath. In addition, the particle motion does not interfere the flow filed. Results of at least some of these simulations are depicted with reference to FIGs. 21-22.

[0164] Residence time distribution (RTD) analyses were performed to evaluate the amount of time that the NAs have spent in the channel. It was assumed that a longer residence time allows the molecule to have a higher possibility of making a contact with the interior walls of the collection device, which presumably also brings a higher tendency of the sample being collected. To consider the difference in volume of each design, The RTD analysis was normalized by following equations.

-I ΘΕ(θ)άθ

Jo

∞

(Θ - e_m)²E(e)de

where t and Θ are time and its dimensionless form. Θ is normalized by τ (V/Q; volume and volume flow rate). Cm and C_out are the particle concentration at inlet and outlet, respectively. [0165] Under ideal conditions, all molecules may spend the same amount of time in the channel. However, the actual residence time may be varied where recirculation of flow exists. In such cases, the variance of the residence time will be greater since the molecules will spend different time in the channel. Results of at least some of these simulations are depicted with reference to FIG. 23.

[0166] The foregoing description of the embodiments, including illustrated embodiments, has been presented only for the purpose of illustration and description and is not intended to be exhaustive or limiting to the precise forms disclosed. Numerous modifications, adaptations, and uses thereof will be apparent to those skilled in the art.

[0167] As used below, any reference to a series of examples is to be understood as a reference to each of those examples disjunctively (e.g., "Examples 1-4" is to be understood as "Examples 1, 2, 3, or 4").

[0168] Example 1 is a sample collection device comprising a sample chamber including an inlet for accepting an aerosol sample and an outlet; an array of protrusions extending from one or more walls of the sample chamber; and a window located in a wall of the sample chamber for exposing the sample chamber to an exterior of the device.

[0169] Example 2 is the device of example 1, wherein the one or more walls of the sample chamber are made of plasmonic materials coated with a protective layer.

[0170] Example 3 is the device of example 2, wherein the protective layer is made of

Si02 or A1203.

[0171] Example 4 is the device of examples 1-3, wherein the array of protrusions includes a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

[0172] Example 5 is the device of examples 1-4, wherein the array of protrusions includes protrusions arranged to facilitate formation of standing waves within the sample chamber.

[0173] Example 6 is the device of examples 1-5, further comprising PCR reagents preloaded into the sample chamber.

[0174] Example 7 is the device of examples 1-6, further comprising a plurality of

DNA primers, wherein the plurality of DNA primers comprises a first primer preloaded into a first region of the sample chamber and a second primer preloaded into a second region of the sample chamber.

[0175] Example 8 is a method, comprising passing an aerosolized sample through a sample chamber of a collection device, wherein passing the aerosolized sample through the sample chamber includes depositing genetic material on internal surfaces of the sample chamber; placing the collection device in a polymerase chain reaction (PCR) machine; thermal cycling the collection device in the PCR machine; and measuring emitted radiation from the collection device.

[0176] Example 9 is the method of example 8, wherein the internal surfaces of the sample chamber of the collection device include plasmonic materials coated with a protective layer.

[0177] Example 10 is the method of example 9, wherein the protective layer is made of Si02 or A1203.

[0178] Example 11 is the method of examples 8-10, wherein the sample chamber of the collection device comprises a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

[0179] Example 12 is the method of examples 8-11, wherein passing the aerosolized sample through the sample chamber includes inducing a standing wave within the sample chamber, and wherein the internal surfaces of the sample chamber are arranged to facilitate formation of the standing wave within the sample chamber.

[0180] Example 13 is the method of examples 8-12, further comprising preloading the sample chamber with PCR reagents.

[0181] Example 14 is the method of examples 8-13, further comprising preloading the sample chamber with a plurality of DNA primers, wherein preloading the sample chamber with the DNA primers includes preloading a first primer into a first region of the sample chamber and preloading a second primer into a second region of the sample chamber.

[0182] Example 15 is a system, comprising a collection device comprising: sample chamber comprising an inlet for accepting an aerosol sample and an outlet; an array of protrusions extending from one or more walls of the sample chamber; and a window located in a wall of the sample chamber for exposing the sample chamber to an exterior of the device; a polymerase chain reaction (PCR) machine for accepting the collection device and performing PCR amplification on the collection device; and an analysis machine for accepting the collection device and measuring an optical signal emitted from the collection device.

[0183] Example 16 is the system of example 15, wherein the one or more walls of the sample chamber are made of plasmonic materials coated with a protective layer.

[0184] Example 17 is the system of example 16, wherein the protective layer is made of Si02 or A1203.

[0185] Example 18 is the system of examples 15-17, wherein the array of protrusions comprises a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

[0186] Example 19 is the system of examples 15-18, wherein the array of protrusions includes protrusions arranged to facilitate formation of standing waves within the sample chamber.

[0187] Example 20 is the system of examples 15-19, wherein the collection device further comprises PCR reagents preloaded into the sample chamber.

[0188] Example 21 is the system of examples 15-20, wherein the collection device further comprises a plurality of DNA primers, wherein the plurality of DNA primers comprises a first primer preloaded into a first region of the sample chamber and a second primer preloaded into a second region of the sample chamber.

Claims

Claims What is claimed is:

1. A sample collection device comprising:

a sample chamber including an inlet for accepting an aerosol sample and an outlet; an array of protrusions extending from one or more walls of the sample chamber; and a window located in a wall of the sample chamber for exposing the sample chamber to an exterior of the device.

2. The device of claim 1, wherein the one or more walls of the sample chamber are made of plasmonic materials coated with a protective layer.

3. The device of claim 2, wherein the protective layer is made of S1O2 or A1₂0₃.

4. The device of claim 1, wherein the array of protrusions includes a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

5. The device of claim 1, wherein the array of protrusions includes protrusions arranged to facilitate formation of standing waves within the sample chamber.

6. The device of claim 1, further comprising PCR reagents preloaded into the sample chamber.

7. The device of claim 1, further comprising a plurality of DNA primers, wherein the plurality of DNA primers comprises a first primer preloaded into a first region of the sample chamber and a second primer preloaded into a second region of the sample chamber.

8. A method, comprising:

passing an aerosolized sample through a sample chamber of a collection device, wherein passing the aerosolized sample through the sample chamber includes depositing genetic material on internal surfaces of the sample chamber;

placing the collection device in a polymerase chain reaction (PCR) machine;

thermal cycling the collection device in the PCR machine; and

measuring emitted radiation from the collection device.

9. The method of claim 8, wherein the internal surfaces of the sample chamber of the collection device include plasmonic materials coated with a protective layer.

10. The method of claim 9, wherein the protective layer is made of S1O2 or A1₂0₃.

11. The method of claim 8, wherein the sample chamber of the collection device comprises a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

12. The method of claim 8, wherein passing the aerosolized sample through the sample chamber includes inducing a standing wave within the sample chamber, and wherein the internal surfaces of the sample chamber are arranged to facilitate formation of the standing wave within the sample chamber.

The method of claim 8, further comprising preloading the sample chamber with PCR

14. The method of claim 8, further comprising preloading the sample chamber with a plurality of DNA primers, wherein preloading the sample chamber with the DNA primers includes preloading a first primer into a first region of the sample chamber and preloading a second primer into a second region of the sample chamber.

15. A system, comprising:

a collection device comprising:

a sample chamber comprising an inlet for accepting an aerosol sample and an outlet;

an array of protrusions extending from one or more walls of the sample chamber; and

a window located in a wall of the sample chamber for exposing the sample chamber to an exterior of the device;

a polymerase chain reaction (PCR) machine for accepting the collection device and performing PCR amplification on the collection device; and

an analysis machine for accepting the collection device and measuring an optical signal emitted from the collection device.

16. The system of claim 15, wherein the one or more walls of the sample chamber are made of plasmonic materials coated with a protective layer.

17. The system of claim 16, wherein the protective layer is made of S1O2 or A1₂0₃.

18. The system of claim 15, wherein the array of protrusions comprises a set of upper protrusions extending from a top wall of the sample chamber and a set of lower protrusions extending from a bottom wall of the sample chamber, and wherein each protrusion of the set of upper protrusions and the set of lower protrusions has a height at least half as tall as a thickness of the sample chamber.

19. The system of claim 15, wherein the array of protrusions includes protrusions arranged to facilitate formation of standing waves within the sample chamber.

20. The system of claim 15, wherein the collection device further comprises PCR reagents preloaded into the sample chamber.

21. The system of claim 15, wherein the collection device further comprises a plurality of DNA primers, wherein the plurality of DNA primers comprises a first primer preloaded into a first region of the sample chamber and a second primer preloaded into a second region of the sample chamber.