Patent Application
20230052202
This invention relates to a cap for a pathogen sample tube. An implementation of the invention enables safer and faster automated handling of samples in a high throughput nucleic acid extraction and Polymerase Chain Reaction (PCR) thermal cycler.
In the prior art, pathogen samples are stored and transported using a simple capped tube; a sample, e.g. a mucus sample, is swabbed from a patient and the swab placed into the tube together with a buffer solution; the tube is then sealed with a conventional cap. The sealed, capped tube is taken to a diagnostics or analysis device, such as a PCR thermal cycler, and a laboratory technician uncaps the tube, manually withdraws (aspirates), e.g. pipettes out, some of the solution and pipettes that solution into a test tube or vial etc. that can be handled by the diagnostics or analysis device. There is considerable scope for human error and hence contamination and failed testing. The process is labour intensive and scales poorly.
A more detailed example: the tube can be used to hold the contents of a nasopharyngeal swab. Once the nasopharynx or other area of interest has been swabbed with a swab to collect mucus, the swab is withdrawn from the nasopharynx. The mucus may contain respiratory viruses such as Respiratory Syncytial Virus (RSV), influenza virus A & B, human parainfluenza virus (HPIV), or SARS-COV-2. The patient or medical practitioner typically uncaps a tube containing a transport buffer solution; the shaft of the swab is then broken off at a snapping point by pressing the shaft end against the inside of the tube wall and the swab head drop to the bottom of the tube and into the transport buffer solution. Viral genetic material is eluted from the pathogens in the mucus held on the swab end into the buffer solution.
Normally, these kinds of sample tubes are then closed and sealed by the patient or medical practitioner using a conventional screw cap; once the capped sample tube reaches a diagnostics or analysis device (e.g. a nucleic acid extraction instrument), the cap is manually removed by a laboratory technician. Some of the liquid buffer sample in the tube is then manually aspirated and pipetted into a tube suitable for testing by the diagnostics or analysis device. When a laboratory technician has to repeat this same procedure many hundreds of times a day, mistakes often occur: these mistakes can lead to failure of the testing, requiring multiple patients to be re-tested, and so leads to delays in diagnosis. Mistakes can also lead to contamination of laboratory equipment and pathogen transmission to the laboratory technician operating the analysis device.
The invention is a cap for a pathogen sample tube, the tube having an open end and the cap being configured to secure the open end of the tube to prevent spillage of any sample stored in the tube;
in which the cap includes a first pierceable protective film section configured to enable an automated pipette or other sample withdrawal system to pierce the protective film section and to aspirate at least some of the sample.
In one implementation, the cap includes a plastic body with a screw thread that securely attaches to a thread around or within the tube; the first pierceable protective film section is a thin aluminium foil with a plastic or polymer coating on one side that is attached across an opening in the plastic body, e.g. by heat welding. The film section can be circular. The cap may also include a second pierceable protective film section lying underneath the first pierceable protective film section; the second pierceable protective film section is again a thin aluminium foil with a plastic or polymer coating on one side that attached across an opening in the plastic body, e.g. by heat welding. The first and second pierceable protective film sections are separated by an air gap that is approximately 2 mm in depth; this structure provides compliance with UN3373 Category B, Packaging Requirements for Biological and Infectious Substances.
This approach removes the need for the technician to have to manually remove the cap in order to be able to withdraw some or all of the sample from within the tube. It is hence safer, allows for faster processing of samples and more reliable than conventional approaches. The structure of the cap makes it far more secure and reliable than a simple rubber septum and far less likely to snag against or interfere with the operation of automated pipette or other sample withdrawal system.
Further details are in the Appendix.
The accompanying Figures show various implementations of the invention.
Several implementations of this invention will now be described. The pathogen sample system implemented by this invention provides a safe way to transport and process a tube containing a transport buffer or any animal or human bodily fluid or other tissue sample, or plant material (we will refer to these as ‘samples’) that may contain highly infectious pathogens (e.g. viruses, parasites, bacteria, bacteriophages or funguses).
As an example, the tube can hold the contents of a nasopharyngeal swab which has been used to sample mucus from the nasopharynx; the swab and mucus may contain respiratory viruses such as RSV, influenza virus A & B, parainfluenza virus or SARS-COV-2.
Normally, conventional kinds of sample tubes are closed and sealed using a simple plastic screw cap; once the sample tube reaches a diagnostics or analysis device, such as a nucleic acid extraction platform, the cap is manually removed; the sample in the tube is then manually aspirated and pipetted into a tube suitable for testing by the diagnostics or analysis device. Human error can arise during these manual processes, risking contamination of the person operating the analysis device, and mistakes that require testing on the patient to be repeated.
The primary implementation of the invention is shown in
We will now describe the structure of the cap 1 that ensures safe transportation of the sample 3, 4 in the tube 2 and eliminates the need for the technician to have to manually remove the cap 1 from tube 2 in order to withdraw the transport buffer solution 3 from tube 2. As noted above, the cap 1 does not need to be removed from tube 2 to enable its contents 3 to be transferred into the test tube or other container used in the diagnostics or analysis device: instead, as shown in the cap cross-section in
The pierceable film is, in one implementation, a thin aluminium foil, approximately 25 microns thick, with a thin lacquer coating on its upper side and a co-extrusion coating (e.g. a polymer coating) on the lower side; the film provides a barrier to light, water vapour, oxygen, and is tamper evident. It is designed to be readily pierced by a pipette tip used in the diagnostics or analysis device; this pipette tip can be a disposable tip. Other material combinations are possible, such as a film that is made entirely of a thin plastic or polymer film. The plastic film may be, without limitation, polytetrafluoroethene (PTFE), polyethylene, polypropylene, a poly(meth)acrylate, polyethylene terephthalate (PET) or acrylonitrile butadiene styrene (ABS).
The pierceable film is, in this implementation, a disc that forms the central, circular section of the cap 1; in one implementation, it is approximately 11.6 mm in diameter. A circular ridge surrounds the disc, protecting the disc from being inadvertently damaged.
There can be two parallel pierceable film discs in the cap; an upper disc 5A and a lower disc 5B, separated by a small gap 6 (e.g. an air gap); in one implementation, the lower disc 5B is slightly smaller than the upper disc 5A (e.g. 9.4 mm in diameter) and the air gap 6 is approximately 2.2 mm; this enables the lower disc 5B to be heat welded into the cap 1 from above, and then the larger disc 5A to be heat welded to the cap 1 from above. If the discs 5A, 5B were the same size, then you would need to heat weld the lower disc from below and the upper disc from above.
Both films 5A, 5B may be made of the same material and hence have the same properties. Alternatively, the second, lower pierceable film 5B may be a septum sealing film made generally from silicone or butyl rubber. This is acts as a self-healing or self-sealing film once the sample has been aspirated and the pipette or needle removed; it re-seals the tube in order to prevent leakage of the pathogen into the platform interior from an otherwise open tube. The rubber film is suitably not scored or otherwise weakened in a way that may compromise the film's ability to re-seal.
Having 2 layers of pierceable film above the sample greatly increases safety; if there were just a single film layer, and that were accidentally punctured through mishandling, then samples (and pathogens) could escape. By providing two separate film layers, that risk is greatly reduced. It also provides compliance with UN3373 Category B (Packaging Requirements for Biological and Infectious Substances; United Nations Economic Commission for Europe (UNECE) European Agreement concerning the International Carriage of Dangerous Goods by Road ADR applicable as from 1 Jan. 2015).
Because the pierceable film discs 5 are centrally positioned in the cap 1, a standard autopipette platform will accurately lower its pipettes through the centre of each disc; this requires no re-programming of the autopipette platform. Where the tube includes a swab, the swab is designed to sink to the bottom of the tube, as shown in
In some embodiments, the cap has an upper plastic film and a lower rubber film. The present inventors have surprisingly found that such an arrangement allows for the rubber film to be pierced by a glass or plastic pipette such that sufficient air can enter the tube, thereby allowing some or all of the sample to be aspirated out.
In some embodiments, the upper plastic film is a pre-cut plastic film. The present inventors have surprisingly found that efficient automated aspiration with glass or plastic pipettes can be achieved with a combination of an upper pre-cut plastic film and a lower rubber film.
After the swab head 4 is added to the tube 2, the tube 2 is then fully sealed by screwing or clipping together the specialised cap 1 on to the mouth of the tube. The cap has a central tapered deformable cylindrical section 8 that acts to bung the cap 1 to prevent leaks. An internal annular sealing surface 9 inside the cap 1 seals against the top 12 of the tube 2 when the when the cap 1 is fully closed onto the tube 2 by turning the cap on its internal thread 15, which engages with tube thread 16.
The cap 1 may lock on to the tube so that it cannot be readily removed, using a mechanical lock shown in
Also, as the tab 20 clicks into place below annular ridge 17, annular sealing surface 9 in the cap seals against the annular top 12 of the tube 2. Accurate, matching spacing of the tube thread 16 from annular ridge 17 and also of cap thread 15 from tab 20 is required.
This specialised cap with one (or more) pierceable film sections 5 can be part of the kit supplied to enable a swab to be taken; the kit could then include (a) a tube 2 with a buffer solution 3; the buffer solution is covered with either a protective plastic film 25 to prevent spillage or a simple, conventional, disposable cap (not shown); (b) the specialised cap 1 with a pierceable film 5; the simple cap 1 is screwed or attached to the tube 2 for storage and transport to the end-user of the swab after a sample is taken; (c) a swab 10 made up.
Note that the locking cap 1 shown in
Both the locking and non-locking versions of the specialised cap 1 come in two further variants. The first variant of the cap, shown in
The second variant of the cap, shown in
As noted above, a sample is then taken by the user (i) sampling mucus in the nasopharynx using the swab 10; (ii) unscrewing a simple disposable cap 1 off the tube 2 (iii) breaking the swab head 4 off from its shaft 11 by pressing it against the inside wall of the tube 2 and so allowing the swab end 4 to drop into the buffer solution 3; (iv) replacing the simple cap with a specialised cap 1 onto the tube. The system is designed to ensure that the swab head 4, once broken and having absorbed some of the liquid transport buffer 3, sinks sufficiently to the bottom of the tube 2 to ensure the pipette tip in the diagnostics machine does not foul on the swab end 4 when aspirating out some of the sample. The shaft 11 of the swab 10 is made from polystyrene and the flocked swab end 4 is made from nylon. The materials from which the tubes, swabs and caps are selected must be able to withstand heating up to 100 C, in order to inactivate pathogens, e.g. SARS-COV-2 prior to transporting or upon receipt by the test centre, prior to insertion into the platform and the perforating of the seal/s. The same plastics should also be selected in order to withstand refrigeration at 4 C and freezing at both −20 C and −80 C.
As noted above, the system is not limited to handling tubes with swabs in a transport buffer, but can be used wherever a tube contains a sample that needs to be analysed. It can therefore be used wherever any animal or human bodily fluid or other tissue sample, or plant material (which may be liquified prior to analysis) needs to be aspirated by a pipette or needle platform that then transfers the sample into an analysis platform, such as a high throughput nucleic acid extraction and PCR thermal cycler.
Once the cap 1 is securely attached to the tube 2, the tube 2 is then moved to a diagnostics machine: it is placed, together with a number of other similar tubes, in a transportation and handling rack 25 that conforms in size to the ANSI/SLAS (SBS) standard for microplates; this ensures that the rack 25 can be processed by a liquid handling platform or by an analysis device (e.g. PCR thermal cycler or nucleic acid extraction platform) designed to handle standard microplates, such as standard 6×4 array microplates. A rack 25 holding twenty four capped tubes 2 in a 6×4 array is shown in
The rack can also be used where the tubes are moved many miles to a centralised laboratory; in either case, it may be desirable to wrap the rack in sealable plastic bag which together is placed into a conformable sealable carton or box to secure all the tubes in position.
In some cases, heat welding the plastic film across the top of all tubes in the rack, or placing a lid over all the tubes, is desirable.
Each tube 2 has a QR code or other unique ID, typically on its base. The base of the rack then includes an aperture 26 under each tube holder; when a tube is placed into the rack, the QR code is hence visible and can be read by a computer vision system (not shown) in the analytics device, enabling the device to automatically and reliably identify each tube, and hence enabling the results it generates to be automatically associated with each tube.
The rack typically will also be QR coded, or another ID bar coded, and holds twenty four tubes with an interference fit, sufficient to prevent a pipette or other sample withdrawal device, when withdrawing from the tube, from snagging against the pierceable film section or sections and lifting the tube up and out of the rack.
There are other ways to ensure that the capped tubes remain securely in the rack 25 during the insertion and withdrawal of the auto-pipettes. For example, a lid, with 24 holes, can drop down onto the tops of the caps or tubes, securing the caps and tubes against the rack 25 and preventing them from being dislodged by the auto-pipettes. The side of each hole in the lid can include a circular ridge that is shaped to engage with a circular groove 30 (See
Each rack may include one or more locking features that secures the rack onto a baseplate of the auto-pipette or other liquid handling platform; this stops the rack being lifted up when the pipette tips are lifted up and have caught against a pierceable film section 5. One or more simple mating features on the rack, that engage with one or more returns or other corresponding features in the baseplate, may be used.
Some diagnostics machines will hold four of these racks 25, as shown in
The racks are then bulk processed in the diagnostics machine by an auto-pipette system, as shown schematically in
Once the aspiration is complete, the racks are withdrawn from the diagnostics machine. Then, to ensure that the contents of the tubes can be safely disposed of, a single plastic (e.g. polyester) sheet is typically heat bonded over all 24 tubes in a rack (or all 96 if four racks are being simultaneously sealed). The sheet can bond to the circular ridge running around the top of each cap. The entire, sealed rack, can now be lifted, maneuvered and deposited into a biological materials hazard waste bin. Tubes could also or alternatively be singularly resealed using bungs, or caps similar to the simple, conventional caps previously mentioned, or singularly or in strips of 8 be sealed with either an adhesive coated film or a heat welded film.
In addition, the pipette tips used in the diagnostics machine can be plastic or glass disposable pipette tips; because the thin aluminium film is designed to be readily pierced by these plastic or glass disposable pipette tips, there is no need to use costly metal needles or metal pipette tips for the aspiration. The pierceable film(s) may also be large enough so that the complete disposable pipette tip, after use, can be ejected and dropped into the sample tube, through the pierceable film(s), where it is retained for biosecurity and to reduce the volume of waste material.
The pierceable films can be designed to self-seal after the pipette tips have been withdrawn; however, by automatically wrapping the entire rack in plastic, this is not essential.
As noted above, these features eliminate the need for manual uncapping of a tube and the manual pipetting of the buffer solution from the tube and into the different sort of tube used by the analytics device. Manual transfer is normally done by a lab technician unscrewing a standard cap from a tube, then carefully and manually inserting a pipette into the sample/buffer in the tube, to withdraw some of the sample/buffer, and then carefully and manually extracting the pipette and then moving the pipette over to the tubes or wells used by the analysis platform (e.g. a high throughput nucleic acid extraction and PCR thermal cycler) and gently pipetting the sample/buffer out into the well/tube.
It can take a significant time to complete this process for an analysis platform that can handle say 48 or 96 samples simultaneously; this is a major bottle neck to the entire process. With the present system, handling is faster and multiple tubes can be simultaneously and automatically penetrated using a conventional auto-pipette platform; the sample contents of all tubes can then be safely and automatically transferred to the wells/tubes used by the analysis platform.
So if the analysis platform works on 48 samples simultaneously, then in this system, 48 sealed tubes can be presented in an array, and then 48 pipette tips then automatically descend, pierce the tube films, withdraw samples and transfer them into an array of 48 wells/tubes used by the analysis platform, enabling far higher throughput. Further, this approach is more accurate, eliminating manual mis-handling errors that can account for an up to 20% error rate. Because it is fully automated, it eliminates the need for skilled lab technicians for the pipetting and is also safer from the cross-infection perspective, since no lab technician is exposed at the pipetting stage. It can also be undertaken within a fully sealed housing which can be flushed with viricidal or anti-bacterial vapour or ultraviolet light, eliminating the need for a large and costly biosafety certified environment.
In summary, the automated, or robotic handling enabled by this invention:
There are multiple variants of the present invention.
Variant A is that the tube is provided to the end-user pre-filled with buffer solution and the interior of the tube is sealed prior to patient use, e.g. sealed at its mouth, with a plastic, heat welded or glued-in seal that is there to retain the transport buffer within the uncapped tube—i.e. even when the tube is uncapped prior to insertion of the swab, the transport buffer solution cannot spill out. Once the swab has been used to take the sample, the seal can be peeled off or the tip of the swab pushed down to pierce this seal and to pass into the transport buffer solution. The specialised cap described above is then used to seal the tube. The swab contents are then eluted into the transport buffer as above.
Variant B: the specialised cap can be screwed down or fixed on to the tube after the swab has been dropped into it; the cap cannot however be unscrewed in normal use; any attempt to remove the cap will harm or damage the cap, giving clear tamper evidence. This can be important when samples tubes need to adhere to chain of custody rules, e.g. for forensic evidence.
Another variant, variant C, is that the kit supplied to enable a swab to be taken includes (a) a tube with a buffer solution; (b) a standard, solid cap, screwed or attached to the tube; (c) a swab. Once the swab is taken and dropped into the tube and the conventional cap placed back on to the tube, the tube is then moved to a diagnostics machine; it is placed, together with a number of other similar tubes, in a rack that typically holds 24 tubes, as described above. The standard cap on each tube is then replaced (e.g. manually by a technician) with the specialised cap and the rack then moved into the diagnostics machine.
In variant D, shown in
This
Tubes, as that term is used in this specification, may be:
In variant E, the specialised cap includes, on its outer face (facing away from the tube) a socket for the swab shaft. The cap is threaded as a normal tube cap with an internal or external thread which marries up to the thread on the outside of or on the inside of the top of the sample tube. In this example the tube contains a transport buffer and after the swab is taken and contains mucus, the shaft of the swab is shortened by breaking at the pre-determined break point against the inside wall of the tube and may be inserted into the socket that is on the outside of the cap.
In variant F, the cap 1 is internally double threaded 42 so as to be used to seal the tube 2 containing the transport buffer 3 (see
In variant G, on the outside of the cap there may be a single or multiple protruding elements that are similar to a gear tooth. This or these protrusions are positioned in relation to the swab and its position within the tube; the projections are used as a datum point for an auto-pipetting station or test platform to locate the pierceable film section of the tube cap. This enables the pierceable film to be accurately located and pierced by a pipette tip or needle and for the transport buffer with the eluted contents of the swab or the bodily fluid to be aspirated from the tube up in to the needle or pipette tip and thereafter transported safely within the auto-pipette station or test platform, into another container or vessel for further liquid handling, manipulation and testing.
If the swab end is not inserted into a socket in the cap, but simply sinks to the bottom of the buffer solution in the tube, then the pierceable film seal or seals can be centralised in the cap without the need for the single or multiple protrusions on the outside of the cap. The liquid handling system will pierce the foil/s in the centre of the cap, as explained for the primary implementation.
In variant H, shown in
The cap 1 fits and closes accurately in relation to the swab partition 50 and foil section 5; to ensure it is fully closed, a registration projection 41 is moulded in to the cap; when this is aligned with a matching projection 51 on the outside of the tube 2, the tube is fully closed in order to prevent leaks from the cap 1 not being fully tightened down on to the tube 2.
The registration projection 51 or point may be a notch or protrusion on the side of the tube 2 that meets or aligns with a similar feature 41 on the cap when fully closed to ensure that:
The physical notch would be below the external thread of the tube to allow the female thread on the tube to match and seal well with the male thread of the cap.
The dividing wall or partition lies cross the width of the sample tube but only within part of the height of tube, to allow the free circulation of the tube buffer medium around the swab and within the body of the tube. The dividing wall prevents the pipette tip from being blocked, fouled or impeded in anyway, including up and down, by the swab shaft (spindle) or by the absorbent end material of the swab.
Different Sampling Kits are Possible:
Sample Kit 1 includes:
Sample Kit 2 includes:
Sample Kit 3 includes:
Sample Kit 4 includes:
Sample Kit 5 includes:
Sample Kit 6 includes:
All sample kits could also include the push fit cap 24A or the screw fit cap 24C to provide extra protection to the pierceable film 5 during transit.
All kit types will be contained within a polyethylene fiber pouch, e.g. a Tyvek™ pouch, that has been sterilized and all nucleic acid (RNA and DNA) destroyed by filling with ethylene oxide gas if the cap has a single seal or gamma radiation sterilized if it has a double seal where it would be impossible for the ethylene oxide gas to sterilize the air gap between the two foils or seals.
Tubes may:
have a locking feature to allow them to lock into a test tube rack so that they remain locked into the rack when the pipette tip is extracted together with some of the sample buffer
This appendix summarises key feature A implemented in the system, as well as a broad range of optional features. Note that each and all optional features can be combined with Key Feature A, as well as one another.
A cap for a pathogen sample tube, the tube having an open end and the cap being configured to secure the open end of the tube to prevent spillage of any sample stored in the tube; in which the cap includes a first pierceable protective film section configured to enable an automated pipette or other sample withdrawal system to pierce the protective film section and to aspirate at least some of the sample.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2005504.2 | Apr 2020 | GB | national |
| 2009586.5 | Jun 2020 | GB | national |
| 2012737.9 | Aug 2020 | GB | national |
This application is a Continuation-in-Part of International Publication No. PCT/GB2021/050904, filed Apr. 15, 2021, which claims priority to United Kingdom application no. 2012737.9, filed Aug. 14, 2020, United Kingdom application no. 2009586.5, filed Jun. 23, 2020, and United Kingdom application no. 2005504.2. filed Apr. 15, 2020, the entire disclosures of which are hereby incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/GB2021/050904 | Apr 2021 | US |
| Child | 17966709 | US |
