The application, inter alia, provides a method for detecting a target nucleic acid, the method comprising the steps of (a) amplifying a target nucleic acid providing an amplified nucleic acid; (b) bringing the amplified nucleic acid in contact with an immobilized leuco dye; and (c) detecting the presence of the amplified nucleic acid under visible light, wherein the detection of the presence of the amplified nucleic acid is indicative of the presence of the target nucleic acid. In some embodiments, the target nucleic acid is derived from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis. The present invention thus also relates to methods for determining whether a subject suffers from an infection caused by Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis and associated diseases.

Sexually transmitted infections (STIs) are among the most common infectious diseases globally and are associated with significant morbidity and mortality worldwide. According to the World Health Organization (WHO), more than 1 million STIs are acquired every day worldwide. In 2020, the WHO estimated that 374 million new infections were reported for one of four of the following STIs: chlamydia (129 million), gonorrhoea (82 million), syphilis (7.1 million) and trichomoniasis (156 million). Approximately 80% of the newly reported STI cases occur in developing countries, and disproportionately impact women. Since many infected individuals present as asymptomatic, STIs may go undetected for a long time leading to their further spread. If left untreated, STIs can lead to more severe consequences than the initial symptoms of the infection, including blindness, bone deformities, brain damage, cancer, heart disease, long-term reproductive complications, birth defects, and even death. Early and accurate diagnosis of infection is therefore essential to limit the spread and outcomes of the infection and provide patients with timely, appropriate, and effective treatment.

Accurate and reliable diagnostic tests for STIs are widely available in high-income countries and typically provided by healthcare professionals. These tests usually involve a physical examination and laboratory testing of blood, urine and/or swab samples. Given the resources needed for such tests, they remain largely unavailable in developing countries. Moreover, testing facilities in developing countries can be geographically inaccessible and expensive, with results being significantly delayed. There is therefore an urgent and unmet need to provide universally accessible and inexpensive STI testing means.

Point-of-care tests have the potential to transform the prevention and control of STIs by enabling immediate diagnosis and early treatment of infections. Currently, there are several point-of-care tests available for the diagnosis of Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis infections, although these tests differ regarding their performance, turnaround time and cost. The U.S. Food and Drug Administration has currently cleared three rapid tests for chlamydia and gonorrhoea and two for trichomonas. The Xpert® CT/NG assay, produced by Cepheid® is anFDA cleared rapid test for Chlamydia and gonorrhoea, however it has not been waived by the Clinical Laboratory Improvement Amendments (CLIA). This is a cartridge-based assay, relying on molecular Nucleic Acid Amplification Technology (NAATs), which is able to detect nucleic acids from pathogens. The Xpert cartridge combines microfluidic technology with real-time polymerase chain reaction (qPCR) allowing for amplification and detection in 90 minutes. Given the use qPCR, which involves thermocycling and a complex amplification process, the Xpert device is large, cumbersome and expensive, making it unsuitable for resource-limited settings.

A second FDA approved and CLIA waived assay for chlamydia and gonorrhoea is the io device produced by binx health. This assay provides sample results in 30 minutes using a combination of rapid PCR amplification and an electrochemical detection system to diagnose infected patients. Again, the use of PCR and the electrochemical nucleic acid detection system necessitates a sophisticated set-up which is unsuitable for out-of-lab use (US9127308).

Beyond point-of-care tests, one area of technology which has the potential to revolutionize STI testing is the development of at-home self-tests, which could provide rapid results directly to the user without the need to attend a health centre or send samples to a laboratory. Currently, there are no products on the market capable of providing such rapid results at home. One obstacle in the development of such technology is the ability to detect amplified pathogen derived nucleic acids in a few simple steps using minimal equipment that is affordable, convenient and user friendly. At-home self-test methods may also reduce the unnecessary use of antibiotics by patients who cannot confirm whether they are infected.

Traditionally, post-amplified nucleic acids are detected using electrophoresis, a labour-intensive manual processing and instrumentation method. More recent developments provide alternative detection methods, e.g., fluorescence detection of double-stranded DNA (dsDNA) with an intercalating or magnesium-sensitive fluorophore; bioluminescence through pyrophosphate conversion; or turbidity detection of precipitated magnesium pyrophosphate. However, these visual methods typically require long incubation times (> 60 minutes), specific instruments for detection, or are too subtle in the change of signal for robust detection outside of the laboratory. Moreover, the currently available methods require several steps, often executed by the user, before a signal is generated. The current methods may therefore be difficult to use and lead to errors when operated by non-professionals.

There is therefore a need for a simple, user-friendly, reliable, rapid and inexpensive method for the detection of amplified pathogen derived nucleic acids.

Thus, the technical problem underlying the present invention is the provision of improved means and methods for the detection of amplified pathogen derived nucleic acids. The present invention therefore provides means and methods for simple indication or diagnosis that can be done outside of the laboratory at a point-of-care or at-home setting. Furthermore, the present invention provides means and methods for the easy and convenient detection of pathogen derived nucleic acids and the management of infections arising from said pathogens. The above technical problem is solved by the embodiments provided herein and as characterised in the claims. Accordingly, the present invention relates to, inter alia, the following embodiments:

1 . A method for detecting a target nucleic acid, the method comprising the steps of: a) amplifying a target nucleic acid providing an amplified nucleic acid; b) bringing the amplified nucleic acid in contact with an immobilized leuco dye; and c) detecting the presence of the amplified nucleic acid under visible light, wherein the detection of the presence of the amplified nucleic acid is indicative of the presence of the target nucleic acid.

2. The method according to embodiment 1 , wherein the leuco dye is immobilized on a test strip.

3. The method according to embodiment 1 or 2, wherein the leuco dye is immobilized onto a test strip comprising at least one polymer, wherein the at least one polymer is preferably selected from a cellulose acetate, mixed cellulose ester, polycarboxylate, agarose or chitosan polymer.

4. The method according to embodiment 3, wherein the test strip comprises the polycarboxylate polymer or agarose polymer in the form of a nanobead.

5. The method according to embodiment 1 or 2, wherein the leuco dye is immobilized in a reservoir comprising a liquid medium.

6. The method according to any one of embodiments 1 to 5, wherein the amplified nucleic acid is detected upon contact with the leuco dye, such that a leaving group (LG) of the leuco dye dissociates and a colour change can be detected under visible light, wherein the leuco dye is of the general formula (I): wherein R ¹ and R ² are each independently selected from a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, carboxyl group, hydroxy group, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group; LG represents -SO3R ⁸ , -NO3, -NO2, -CN, halogen, -NHR ⁹ , -N(COR ¹⁰ ) (COR ¹¹ ), -SR ¹² , -SSR ¹³ , -OR ¹⁴ , -NHSNH2, -OH or -H, with R ⁸ representing an alkali metal or a hydrogen atom, R ⁹ , R ¹⁰ , R ¹¹ , R ¹² , R ¹³ , R ¹⁴ independently represent an alkyl group, aryl group, acyl group, alkenyl group or alkynyl group. The method according to embodiment 6, wherein the amplified nucleic acid is determined to be present if a visible light signal is detected where the leuco dye is immobilized. The method according to embodiment 6 or 7, wherein the leuco dye of the general formula (I) is one or more dyes selected from methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof. The method according to any one of embodiments 1 to 5, wherein the amplified nucleic acid and leuco dye form a complex which is brought into contact with a nucleophile that is immobilized downstream of the leuco dye, wherein the leuco dye of the complex is of the general formula (II): wherein R ¹ and R ² each independently represent a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, ammonium ion, alkylammonium ion, carboxyl group, hydroxy group, oxocarbenium ion, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group, and/or wherein the immobilized nucleophile comprises sulfite ions, hydrogen sulfite ions, nitrate ions, nitrite ions, cyanide ions, halide ions, nitrogen nucleophiles, sulfur nucleophiles, alkali metal alkoxides, alkali metal hydroxides or hydride nucleophiles. The method according to embodiment 9, wherein the amplified nucleic acid is determined to be present if a visible light signal is detected where the nucleophile is immobilized. The method according to embodiment 9 or 10, wherein the leuco dye of the general formula (II) is one or more dyes selected from methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof. The method according to any one of embodiments 1 to 11 , wherein the target nucleic acid is amplified by a loop-mediated isothermal amplification (LAMP) method. The method according to any one of embodiments 1 to 12, wherein the target nucleic acid is DNA or RNA. The method according to any one of embodiments 1 to 13, wherein the amplified nucleic acid is single or double stranded nucleic acid. The method according to any one of embodiments 2 to 14, wherein the test strip comprises a control line downstream of the immobilized leuco dye and/or immobilized nucleophile. The method according to embodiment 15, wherein the control line comprises an immobilized 3, 3’, 5, 5’ -tetramethylbenzidine. The method according to embodiment 15, wherein the control line comprises a leuco dye immobilized on bentonite clay. The method according to any one of embodiments 1 to 17, wherein the target nucleic acid is bacterial or protozoal DNA. The method according to embodiment 18, wherein the bacterial or protozoal DNA is derived from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis. A device or kit for detecting a target nucleic acid, wherein the device comprises: a) a compartment for the amplification of a target nucleic acid to give an amplified nucleic acid; b) a leuco dye immobilized on a test strip; and c) a flow path for the amplified nucleic acid to be in contact with the immobilized leuco dye. The device or kit according to embodiment 20, wherein the leuco dye is immobilized on a test strip comprising at least one polymer, wherein the at least one polymer is preferably selected from a cellulose acetate, mixed cellulose ester, polycarboxylate, agarose or chitosan polymer. The device or kit according to embodiment 20 or 21 , wherein the test strip comprises the polycarboxylate polymer or agarose in the form of a nanobead. The device or kit according to embodiment 20, wherein the leuco dye is immobilized in a reservoir comprising a liquid medium. The device or kit according to any one of embodiments 20 to 23, wherein the leuco dye is of the general formula (I): wherein R ¹ and R ² are each independently selected from a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, carboxyl group, hydroxy group, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group; LG represents -SO3R ⁸ , -NO3, -NO2, -CN, halogen, -NHR ⁹ , -N(COR ¹⁰ ) (COR ¹¹ ), -SR ¹² , -SSR ¹³ , -OR ¹⁴ , -NHSNH2, -OH or -H, with R ⁸ representing an alkali metal or a hydrogen atom, R ⁹ , R ¹⁰ , R ¹¹ , R ¹² , R ¹³ , R ¹⁴ independently represent an alkyl group, aryl group, acyl group, alkenyl group or alkynyl group. The device or kit according to embodiment 24, wherein a signal is generated where the leuco dye is immobilized by contact between the leuco dye and amplified nucleic acid. The device or kit according to embodiment 20 to 23, wherein the leuco dye is of the general formula

(II): wherein R ¹ and R ² each independently represent a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, ammonium ion, alkylammonium ion, carboxyl group, hydroxy group, oxocarbenium ion, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group.

27. The device or kit according to any one of embodiments 20 to 26, wherein the device or kit comprises at least two compartments for the amplification of a target nucleic acid, at least two test strips comprising immobilized leuco dye and at least two flow paths to contact the amplified nucleic acid with the immobilized leuco dye.

28. A method of diagnosing, and/or prognosing a disease by detecting the presence of a target nucleic acid using the method of any one of embodiments 1 to 19.

29. The method of embodiment 28, wherein the disease is an infectious disease.

30. The method of embodiment 29, wherein the infectious disease comprises one or more selected from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis.

31. A method of treating an infectious disease, wherein the method comprises administering to a subject identified as having or developing an infectious disease using the method of any one of embodiments 1 to 19 or the device or kit of any one of embodiments 20 to 27 an appropriate treatment for said disease.

32. The method of embodiment 31, wherein the infectious disease comprises one or more selected from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis.

Accordingly, in a first embodiment, the invention relates to a method for detecting a target nucleic acid, the method comprising the steps of: a) amplifying a target nucleic acid providing an amplified nucleic acid; b) bringing the amplified nucleic acid in contact with an immobilized leuco dye; and c) detecting the presence of the amplified nucleic acid under visible light, wherein the detection of the presence of the amplified nucleic acid is indicative of the presence of the target nucleic acid.

As such, in a first step of the method of the invention, a target nucleic acid is amplified to provide an amplified nucleic acid.

The term “target nucleic acid”, as used herein, refers to a nucleic acid, preferably RNA or DNA, comprising a sequence known to the skilled person to be comprised in a larger target sequence, for example the genome of a target organism. In one embodiment, the target sequence is thus a sequence comprised in a target organism. It is preferred that the target sequence is a sequence allowing to distinguish between one or more, in particular two or more, in particular three or more, organisms, preferably bacteria or protozoa. As such, it is preferred that the target nucleic acid as used herein is uniquely found in a target organism or, at least, is not part of more than one, in particular two or more organisms to be detected using the methods of the invention.

The term "amplified nucleic acid", as used herein, refers to a nucleic acid product generated by a nucleic acid amplification technique. Nucleic acid amplification techniques are known to the skilled person. Such techniques can be broadly categorised into those requiring thermal cycling and isothermal methods. Methods requiring thermal cycling, such as PCR, transcription mediated amplification (TMA) and nucleic acid sequence-based amplification (NASBA), cycle the nucleic acid sequence amplification procedure through different temperatures (e.g., 95°C for denaturation, 45°C to 68°C for primer annealing and 68°C to 72°C for template extension) during each round of amplification, thereby requiring a thermal cycler for the technique. Isothermal nucleic acid amplification techniques include strand displacement amplification (SDA), loop-mediated isothermal amplification (LAMP), nicking enzyme amplification reaction (NEAR), helicase-dependent amplification (HDA), rolling circle amplification (RCA) and recombinase polymerase amplification (RPA) do not require a thermal cycler. Within the present invention, an isothermal amplification method is preferred. In particular, it is preferred that a LAMP method is used to obtain the amplified nucleic acid in the methods of the invention.

In a second step, subsequent to the step of amplifying a target nucleic acid providing an amplified nucleic acid, the amplified nucleic acid is brought into contact with an immobilized leuco dye.

The term “leuco dye”, as used herein, refers to a dye which is able to switch between two chemical forms; one of which is substantially colorless or white when observed in day light - referred to as the “leuco form” of the leuco dye. The leuco form of the leuco dye typically reacts with another substance to form a colored dye, the second chemical form of the leuco dye. The color-altering phenomenon is typically due to a chemical change, such as through an oxidation reaction. It is to be understood that the term leuco dye, as used herein, encompasses both the leuco form and colored form of the leuco dye. An example of the transformation of a leuco dye from the leuco form to a colored dye is given herein below:

Leuco form Colored dye

The term “bringing into contact”, or grammatical variations thereof, as used herein, refers to a step of allowing a chemical interaction to happen between at least two molecules, e.g. a target molecule and a leuco dye. Within the present invention, this step is meant to allow the interaction between the amplified nucleic acid and an immobilized leuco dye used to determine the presence of a target nucleic acid. The interaction may be, but is not limited to, covalent or non-covalent binding, such as ionic binding, coordinate binding, van der Waals binding and/or pi-pi interaction. The interaction between the nucleic acid and leuco dye may result in the formation of a complex between the leuco dye and nucleic acid. The formation of a complex between the leuco dye and nucleic acid is well described in the art, and may involve a reaction between the two, but not necessarily so. The formation of this complex may result in a color change that is visible to the naked eye and indicative of the presence of the target nucleic acid.

In one embodiment of the invention, the amplified nucleic acid is comprised in a solution which is brought into contact with an immobilized leuco dye.

The term, “detecting under visible light”, or grammatical variations thereof, as used herein, refers to the detection of the presence of a color change by the naked eye under ordinary lighting, preferably without exposure to light other than visible light. It is thus required that the color change of the leuco dye used herein is observable under visible light. As such, detection is simplified and does not require equipment, such as a fluorescence reader commonly employed in other nucleic acid detection methods. By visually observing the presence of a color change, it can be determined whether the amplified nucleic acid and thereby target nucleic acid is present. Specific examples of changes in color include changes in the type of color under visible light (visible light wavelength) and changes in the concentration of color (reflectance) but are not limited to these as long as the changes can be detected under visible light. Exemplary changes in the type of color include, for example, the changes from colorless to green, colorless to blue, colorless to magenta.

The nucleic acid can also be detected by measuring absorbance in the visible light range. Visible light, as used herein, indicates light at wavelengths of 380 nm to 800 nm. The measurement wavelength can be set appropriately according to the dye. It is also possible to assay the nucleic acid concentration in a sample by absorbance measurement. In addition, when an insoluble precipitate of the dye and nucleic acid is formed, the precipitate can be detected with a filter or membrane, or by centrifugation. A dye of a different color may also be mixed in to make it easier to determine the presence or absence of the nucleic acid.

The inventors of the present invention found that the use of an immobilized leuco dye for the detection of an amplified nucleic acid provides surprising benefits over the prior art, in particular it provides a rapid and simple means to determine the presence of a target nucleic acid, for example a target nucleic acid comprised in the genome of a pathogen. Conveniently, within the methods of the present invention, the presence of the target nucleic acid can be detected under visible light with minimal equipment, enabling point-of-care and at-home self-test diagnosis of the presence of a pathogen.

Accordingly, within the present invention, the leuco dye is immobilized, preferably immobilized on a test strip.

The term “test strip”, as used herein, refers to a solid or semi-solid strip comprising a material which allows for capillary flow of a solution along a flow path. Generally, the material is rectangular, and the flow path is axial, however the size and shape of the material is not particularly limited, as long as it allows for capillary flow. The test strip of the present invention may be uniplanar with a single sheet on the test strip, comprising at least one line wherein a leuco dye is immobilized. Alternatively, the test strip may be multiplanar and comprise multiple lines on multiple sheets which are in fluid communication for simultaneous assays for the same or different target analytes from the same or different samples. In preferred embodiments of the invention, the test strip is in fluid communication with the amplification compartment, such that a solution of the amplified nucleic acid may flow along the test strip to at least one line wherein a leuco dye is immobilized. Once the amplified nucleic acid solution flows to the line where the leuco dye is immobilized, a complex is formed between the leuco dye and amplified nucleic acid, which may or may not result in a color change where the leuco dye is immobilized.

The term “immobilized on a test strip”, or grammatical variations thereof, as used herein, refers to the immobilization of a leuco dye on the solid or semi-solid test strip as defined hereinabove. The leuco dye may be immobilized in a solid or liquid state. The immobilization of the leuco dye may be achieved by physical or chemical means. Physical means of immobilization include, adsorption, absorption and entrapment, but are not limited to these methods. Chemical immobilization may involve the covalent linkage of the leuco dye to a material comprised on the test strip but is not necessarily limited to covalent linkage. Furthermore, in preferred embodiments of the invention, the leuco dye is immobilized in a localized and specific line on the test strip, preferably directly downstream of the amplification compartment.

The inventors of the present invention surprisingly found that the method of the present invention allows for a facile “one-step” detection of an amplified nucleic acid from a target nucleic acid by means of a test strip on which a leuco dye is immobilized. This is particularly advantageous for point-of-care and at-home self-tests for the detection of pathogenic infection. The simplistic signal visualization enabled by the use of an immobilized leuco dye on the test strip provides a direct optical readout which can be read and interpreted by the user without the need to consult a healthcare professional. The provision of a test strip with an immobilized detecting reagent additionally allows for the test results to be easily recorded and documented. Another advantage of the test strip design is the ease of manufacture, storage and handling of devices comprising these elements. Furthermore, immobilizing the leuco dye on a test strip improves the stability and shelf-life of the leuco dye, particularly compared to methods where liquid form dyes are employed.

In a further preferred embodiment of the invention, the leuco dye is immobilized onto a test strip comprising at least one polymer, wherein the at least one polymer is preferably selected from a cellulose acetate, mixed cellulose ester, polycarboxylate, agarose or chitosan polymer.

The term “cellulose acetate”, as used herein, refers to a fibrous porous material which may comprise a pure cellulose acetate polymer or modified cellulose acetate polymer. The fibres of the material may be oriented along a particular axis (i.e., aligned), or they may be random.

The term “mixed cellulose ester (MCE)”, as used herein, refers to membrane filters that are composed of a mixture of cellulose nitrate and cellulose acetate. MCE materials are naturally hydrophilic and offer a high degree of internal surface area with uniform pore structure which provides consistent flow and diffusion rates.

The term “polycarboxylate polymer”, as used herein, refers to polyanionic macromolecules comprising carboxylate-terminated polymers. Examples of carboxylate-terminated polymers include, but are not limited to, carboxylated polystyrene, cellulose acetate phthalate (CAP), polyvinyl acetate phthalate (PVAP), various grades of hydroxypropyl methylcellulose phthalate and various grades of methacrylic acid copolymers.

The term "agarose", as used herein, refers to the neutral gelling fraction of agar, consisting of a linear polymer based on the -(1 -^3)-p-D-galactopyranose-(1 — >4)-3,6- anhydro-a-L-galactopyranose units. Agarose is typically high in molecular weight, which is about 120,000 and low in sulphate. The agarose polymer of the present invention is preferably activated to comprise an aldehyde group which is commonly referred to as an “aldehyde-activated agarose” or “polyaldehyde-activated agarose” in the art. The provision of aldehyde groups on the agarose polymer allow for the linkage of the polymer to a variety of chemical moieties, including amine groups. Alternative activated forms of agarose polymers are well described in the art, and may for example include cyanogen halide activated agarose, N-hydrosuccinimde activated agarose, epoxy activated agarose and amine activated agarose. A person skilled in the art is aware of the various activated agarose forms which may be suitable for the present invention.

The term “chitosan polymer” or “chitosan membrane”, as used herein, refers to a linear polysaccharide composed of randomly distributed 0-(1 — >4)-linked D-glucosamine (deacetylated unit) and N-acetyl-D-glucosamine (acetylated unit). In preferred embodiments of the invention, the leuco dye is immobilized on the chitosan polymer by a covalent linkage between the amine of the chitosan polymer and an amino group of the leuco dye.

Within the present invention, it was found that the immobilization of the leuco dye on a cellulose acetate, mixed cellulose ester, polycarboxylate, agarose or chitosan polymer is particularly advantageous to immobilize the leuco dye in a localized line of the test strip. Generally, the polymer used should allow liquid to flow on or through the strip. It should be understood that the test strip of the present invention may use a variety of polymers and materials which should be in fluid flow communication/contact or capable of being brought into fluid flow communication/contact. The strip should have sufficient inherent strength or additional strength can be provided by a supplemental support such as a plastic backing upon which porous or bibulous strip components are attached.

In some embodiments of the invention, the test strip comprises the polycarboxylate or agarose polymer in the form of a nanobead.

In preferred embodiments of the invention, the polycarboxylate polymer nanobead comprises carboxylated polystyrene or carboxylate-terminated polystyrene. In further preferred embodiments, the nanobead has a pore size of 0.5 pm, 0.75 pm, 1 .0 pm, 2.0 pm, 3.0 pm, most preferred is a diameter of 3.0 pm, however, the diameter is not particularly limited.

In another preferred embodiment of the invention, the agarose nanobeads are aldehyde activated nanobeads with a uniform size in the range of 50 to 150 pm. The use of polycarboxylate or agarose polymer nanobeads in the present invention was found to improve the detection performance of the test strip. More specifically, the inventors found that the use of nanobeads prevents leaching and improves the stability of the leuco dye. This is typically achieved by the covalent linkage of the dye to the nanobead but may also be achieved by any other means of chemically or physically immobilizing the leuco to the nanobead. Furthermore, the use of nanobeads improves the visibility of the color change, due to the availability of a larger surface area for binding, thus improving the sensitivity of detection assays. A further advantage of the use of nanobeads is the potential to tune and optimize the flow rate on the test strip by selecting nanobeads with various pore sizes.

In some embodiments of the invention, the leuco dye is immobilized in a reservoir comprising a liquid medium.

Within the present invention, the immobilization of the leuco dye within a reservoir comprised on the test strip may be advantageous for the efficient mixing of the solution of amplified nucleic acid and a solution of leuco dye comprised in a reservoir, thereby potentially optimising the contact made between the leuco dye and amplified nucleic acid which may have an impact on the signal intensity. The liquid medium comprising the leuco dye of the present invention may include aqueous solutions such as distilled or purified water or buffer solutions but is not particularly limited.

In some embodiments, it is preferred that the amplified nucleic acid is detected upon contact with the leuco dye, such that a leaving group (LG) of the leuco dye dissociates and a colour change can be detected under visible light, wherein the leuco dye is of the general formula (I): wherein R ¹ and R ² are each independently selected from a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, carboxyl group, hydroxy group, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group; LG represents -SO3R ⁸ , -NO3, -NO2, -CN, halogen, -NHR ⁹ , -N(COR ¹⁰ )(COR ¹¹ ), -SR ¹² , -SSR ¹³ , -OR ¹⁴ , -NHSNH2, -OH or -H, with R ⁸ representing an alkali metal or a hydrogen atom, R ⁹ , R ¹⁰ , R ¹¹ , R ¹² , R ¹³ , R ¹⁴ independently represent an alkyl group, aryl group, acyl group, alkenyl group or alkynyl group.

In some embodiments of the present invention, the amplified nucleic acid is determined to be present if a visible light signal is detected where the leuco dye is immobilized. The inventors of the present invention found that by contacting a nucleic acid with an immobilized leuco dye of general formula (I), a leaving group on the leuco form of the leuco dye dissociates by interaction with the amplified nucleic acid, resulting in a color change that can be detected under visible light. The visible signal may be assessed either visually or by optical detection devices, such as a smartphone camera capable of reading storing and transmitting the test result.

In preferred embodiments of the invention, the leuco dye of the general formula (I) is one or more dyes selected from methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof.

As preferably understood herein, methyl green of the general formula (I) is a compound according to formula:

As preferably understood herein, basic fuchsin of the general formula (I) is a compound according to formula:

As preferably understood herein, acid fuchsin of the general formula (I) is a compound according to formula:

As preferably understood herein, crystal violet of the general formula (I) is a compound according to formula:

As preferably understood herein, malachite green of the general formula (I) is a compound according to formula:

Where an overall positive charge possessed by the compounds of general formula (I), particularly methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof, the positive charge is balanced by a necessary counterion or counterions. The counterion(s) may be the counterion(s) indicated hereinabove and represented by the abbreviation LG, however the counterion(s) of the present invention is not particularly limited and may include counterions well described in the art.

In further embodiments of the present invention, the amplified nucleic acid and leuco dye form a complex which is brought into contact with a nucleophile that is immobilized downstream of the leuco dye, wherein the leuco dye of the complex is of the general formula (II): wherein R ¹ and R ² each independently represent a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, ammonium ion, alkylammonium ion, carboxyl group, hydroxy group, oxocarbenium ion, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group, and/or wherein the immobilized nucleophile comprises sulfite ions, hydrogen sulfite ions, nitrate ions, nitrite ions, cyanide ions, halide ions, nitrogen nucleophiles, sulfur nucleophiles, alkali metal alkoxides, alkali metal hydroxides or hydride nucleophiles.

In further embodiments of the present invention, the amplified nucleic acid is determined to be present if a visible light signal is detected where the nucleophile is immobilized.

The inventors of the present invention found that contacting a leuco dye of general formula (II) with the amplified nucleic acid results in the formation of a complex, which can then be contacted with a nucleophile downstream of the immobilized leuco dye. In the presence of the leuco dye nucleic acid complex, a visible light signal in the form of a color change is observed where the nucleophile is immobilized.

The inventors of the present invention have found that when the dye of general formula (II) is contacted with the target nucleic acid solution prior to the onset of the amplification reaction, the dye of general formula (II), may, in some embodiments, change color (e.g., change from a colored form to a colorless form) as a result of a reaction with a compound comprised in the solution, for example, Tris comprised in a buffer solution (or any other basic compounds comprised in e.g., buffer solutions that are well known to the skilled person). The reaction of the dye of general formula (II) with a compound comprised in the buffer can result in the formation of a compound of general formula (I), where LG is comprised of the compound comprised in the solution. Once amplification of the target nucleic acid has taken place, the amplicons then react with the compound of general formula (I), resulting in the dissociation of the LG and a change in color. However, this reaction is typically slow taking around 60 minutes for the color change to be detected under visible light. In embodiments where the dye is immobilized, and the amplification takes place (providing the amplified nucleic acid) prior to contacting the dye of general formula (II), the reaction with a compound comprised in the solution, e.g., the buffer solution, does not take place and a nucleic acid-dye of formula (II) complex is formed which may flow downstream to a location where the nucleophile is immobilized. In preferred embodiments, once the nucleic acid-dye of formula (II) (i.e., when the pathogen is present in the sample and amplification has taken place) is in contact with the immobilized nucleophile a color change may be observed due to the reaction of the nucleic acid-dye of formula (II) complex and nucleophile. In some embodiments, when the target nucleic acid is not present in the sample and amplification does not take place, contact between the solution comprising the sample and the dye of general formula (II) may result in the reaction of said dye with a compound comprised in said solution, resulting in the formation of a compound of general formula (I). In preferred embodiments, when the compound of general formula (I) is contacted with an immobilised nucleophile, no color change is observed under visible light.

In preferred embodiments of the present invention, the leuco dye of the general formula (II) is one or more dyes selected from methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof.

As preferably understood herein, methyl green of the general formula (II) is a compound according to formula:

As preferably understood herein, basic fuchsin of the general formula (II) is a compound according to formula:

As preferably understood herein, acid fuchsin of the general formula (II) is a compound according to formula:

As preferably understood herein, crystal violet of the general formula (II) is a compound according to formula:

As preferably understood herein, malachite green of the general formula (II) is a compound according to formula:

Where an overall positive charge possessed by the compounds of general formula (I), particularly methyl green, basic fuchsin, acid fuchsin, crystal violet, malachite green or derivatives thereof, the positive charge is balanced by a necessary counterion or counterions. The counterion(s) may be the counterion(s) indicated hereinabove and represented by the abbreviation LG, however the counterion(s) of the present invention is not particularly limited and may include counterions well described in the art.

In a preferred embodiment of the present invention, the target nucleic acid is amplified by a loop- mediated isothermal amplification (LAMP) method.

Within the method of the present invention, It is preferred that amplification is carried out at a constant temperature, in particular using a LAMP method. In some embodiments of the invention, the LAMP method uses 6 primer oligonucleotides comprising a forward outer primer (F3), backward outer primer (B3), forward inner primer (FIP), backward inner primer (BIP), loop primer forward (LF) and loop primer backward (LB) and a polymerase with strand displacement activity to identify a target region on the target nucleic acid. These terms are commonly used in methods related to LAMP, such as those described by Nagamine et al. 2002. Molecular and Cellular Probes 16. 223-229. The F3 and B3 primers are strand invasion oligonucleotides used for the elongation step. The addition of loop primers significantly accelerates amplification, increasing sensitivity and reducing reaction time.

The inventors of the present invention found that amplification of the target nucleic acid by a LAMP method is advantageous since it does not require thermal cycling which necessitates large and complicated equipment to produce detectable amounts of amplified nucleic acid. It is well understood in the art that the LAMP method is a highly sensitive and specific diagnostic method. The use of the LAMP method therefore is well suited for point-of-care and at-home self-tests, which require that the method is fast, efficient and useable by non-medical professionals.

In some embodiments of the present invention, the target nucleic acid is DNA or RNA.

In some embodiments of the present invention, the amplified nucleic acid is single or double stranded nucleic acid.

In some embodiments of the present invention, the test strip comprises a control line downstream of the immobilized leuco dye and/or immobilized nucleophile.

The term “control line”, as used herein, refers to a region of the test strip, generally downstream of the test line(s), which is used to indicate that the sample has flowed through the test line(s). Generally, the control line comprises one or more immobilized reagents capable of providing an indication that the sample has passed through the test lines. The skilled person is aware of typical reagents comprised in the control line of test strips. In preferred embodiments of the invention, the control line provides a visible signal upon contact with the sample. The present invention may comprise at least one, and optionally more control lines, but does not necessarily do so.

In one embodiment of the invention, the control line comprises an immobilized 3, 3’, 5,5’- tetramethylbenzidine.

Immobilized 3,3’,5,5’-tetramethylbenzidine (TMB) is a typical reagent used for control lines on test strips. TMB is oxidised by the enzyme horseradish peroxidase, which produces a visible color change from colorless to blue. In preferred embodiments of the invention, the primers used for the amplification of the target nucleic acid would comprise horseradish peroxidase, thereby producing amplified nucleic acids containing horseradish peroxidase. Post-amplified samples containing horseradish peroxidase which flow to the control line react with TMB and provide a visible signal that the sample has flowed through the test strip and test lines(s).

In some embodiments of the invention, TMB is immobilized on a cellulose acetate, mixed cellulose ester or chitosan polymer. The immobilization may be, but is not limited to, chemical immobilization via covalent bond formation, or physical immobilization via adsorption or absorption.

In a preferred embodiment of the invention, the control line comprises a leuco dye immobilized on bentonite clay.

The term “bentonite clay”, as used herein, refers to an absorbent swelling clay comprising mainly of montmorillonite - a soft phyllosilicate group of minerals.

The inventors of the present invention surprisingly found that a solid mixture comprising the bentonite clay and leuco dye immobilized on a test strip may act as reagents capable of providing a visible signal on the control line. The inventors found that a control line comprising a mixture of bentonite clay and leuco dye provides a visible signal upon contact with a sample solution indicating that a leaving group on the leuco dye dissociates upon interaction with the solution. A color change is observed irrespective of whether the sample contains the amplified nucleic acid.

In one embodiment of the invention, the target nucleic acid is bacterial or protozoal DNA.

In preferred embodiments of the invention, the bacterial or protozoal DNA is derived from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis.

The method of the present invention is particularly suitable for the detection of target nucleic acids derived from Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium or Trichomonas vaginalis. The method of the present invention therefore provides a simple and efficient means for detecting a signal from the nucleic acid originating from a sexually transmitted pathogenic organism and indicating to the user whether or not they have been infected.

In one embodiment of the invention, the invention provides a device or kit for detecting a target nucleic acid, wherein the device comprises: a) a compartment for the amplification of a target nucleic acid to give an amplified nucleic acid, b) a leuco dye immobilized on a test strip, c) a flow path for the amplified nucleic acid to be in contact with the immobilized leuco dye. The term “compartment for amplification”, as used herein, refers to any structure or container which may be used for the amplification of the target nucleic acid. The material of the container is not particularly limited but may for example be comprised of a plastic material. In preferred embodiments of the invention, the amplification compartment is in fluidic communication with the test strip, to enable the detection of the amplified nucleic acid.

Advantageously, the device of the present invention will be suitable for providing a "one-step" detection of nucleic acids derived from pathogens causing STIs. In particular, after the amplification of the target nucleic acid, the amplified sample may be flowed through the test strip to provide a visual signal which directly indicates the presence or absence of a pathogen derived nucleic acid, without performing any additional steps.

In some embodiments of the invention, the device or kit of the invention contains a leuco dye which is immobilized on a test strip comprising at least one polymer, wherein the at least one polymer is preferably selected from a cellulose acetate, mixed cellulose ester, polycarboxylate, agarose or chitosan polymer.

In some embodiments of the device or kit contains a test strip comprising the polycarboxylate polymer or agarose in the form of a nanobead.

In some embodiments of the device or kit, the leuco dye is immobilized in a reservoir comprising a liquid medium.

In some embodiments of the device or kit, the leuco dye is of the general formula (I): wherein R ¹ and R ² are each independently selected from a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, carboxyl group, hydroxy group, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group; LG represents -SO3R ⁸ , -NO3, -NO2, -CN, halogen, -NHR ⁹ , -N(COR ¹⁰ ) (COR ¹¹ ), -SR ¹² , -SSR ¹³ , -OR ¹⁴ , -NHSNH2, -OH or -H, with R ⁸ representing an alkali metal or a hydrogen atom, R ⁹ , R ¹⁰ , R ¹¹ , R ¹² , R ¹³ , R ¹⁴ independently represent an alkyl group, aryl group, acyl group, alkenyl group or alkynyl group. In some embodiments of the device or kit a signal is generated where the leuco dye is immobilized by contact between the leuco dye and amplified nucleic acid.

In some embodiments of the device or kit the leuco dye is of the general formula (II): wherein R ¹ and R ² each independently represent a substituted or unsubstituted aryl group; R ³ , R ⁴ , R ⁵ , R ⁶ , R ⁷ independently represent a hydrogen, halogen, amino group, alkylamino group, ammonium ion, alkylammonium ion, carboxyl group, hydroxy group, oxocarbenium ion, sulfo group, nitro group, nitrile group, isonitrile group, amido group, alkyl group, aryl group, alkenyl group, alkynyl group, alkoxy group, aryloxy group, alkylthio group, arylthio group, arylamino group, acyl group, alkoxycarbonyl group, aryloxycarbonyl group, alkylsulfonyl group or arylsulfonyl group.

I n some embodiments, the device or kit comprises at least two compartments for the amplification of a target nucleic acid, at least two test strips comprising immobilized leuco dye and at least two flow paths to contact the amplified nucleic acid with the immobilized leuco dye.

Within the present invention, the target nucleic acid may be comprised in a sample obtained from a human subject (e.g. tissue sample, bronchoalveolar lavage, bronchial wash, pharyngeal exudate, tracheal aspirate, blood, serum, plasma, bone, skin, soft tissue, intestinal tract specimen, genital tract specimen, breast milk, lymph, cerebrospinal fluid, pleural fluid, sputum, urine, a nasal secretion, tears, bile, ascites fluid, pus, synovial fluid, vitreous fluid, vaginal secretion, semen and/or urethral tissue). In preferred embodiments of the invention, the sample comprising the target nucleic acid is obtained from urine, urethral swab, endocervical swab or vaginal swab.

Figure 1 Shows the basic concept of the device of the present invention comprising a LAMP compartment (or well) and a lateral flow test strip with a test zone and control zone. The test zone herein would comprise an immobilized leuco dye of general formula (I), wherein a leaving group of the leuco dye dissociates upon interaction with the amplified nucleic acid. The interaction of the leuco dye and nucleic acid would produce a visible light signal.

Figure 2 Shows the basic concept of the device of the present invention comprising a LAMP compartment (or well) and a lateral flow test strip with two test zones and control zone. The first test zone comprises the leuco dye of general formula (II) which forms a complex with the amplified nucleic acid, the solution of which then flows downstream to a second test zone comprising an immobilized nucleophile. A visible light signal where the nucleophile is immobilized indicates the presence or absence of the amplified nucleic acid.

Figure 3 Shows the immobilization of basic fuchsin on a chitosan polymer.

Examples

General procedure for the non-chemical immobilization ofleuco-dye on polymeric material

A strip of polymeric material was dipped into a solution of leuco-dye and was allowed to incubate for 15- 30 min at room temperature. Subsequently, the polymeric membrane was removed and allowed to dry for another 30 min. Note that the polymeric material may gain the colour of the leuco-dye.

Example of immobilization of methyl green - sodium sulfite leuco-dye of general formula (I) on cellulose acetate

A strip of cellulose acetate membrane was dipped into a solution of leuco-dye and was allowed to incubate for 15-30 min at room temperature. Subsequently, the cellulose acetate membrane was removed and allowed to dry for another 30 min. Note that here methyl green-sodium sulfite leuco-dye (of general formula (I)) is colourless therefore, the cellulose acetate retained its initial colour.

Example of immobilization of methyl green-sodium sulfite leuco-dye of general formula (I) immobilized on polycarboxylate nanobeads

Polycarboxylate nanobeads were added to a solution of methyl green-sodium sulfite based leuco-dye. The mixture was allowed to incubate for 15-30 min at room temperature. Subsequently, the polycarboxylate nanobeads were allowed to dry for another 30 min. Note that here methyl green-sodium sulfite leuco-dye (of general formula (I)) is colourless therefore, the polycarboxylate nanobeads retain their initial colour.

General procedure for the chemical immobilization ofleuco-dyes on polymeric material

A Functionalized polymeric material is conjugated to a functionalized dye through a chemical reaction. Subsequently, the obtained polymeric material is reacted to a nucleophile (e.g., sodium sulfite) resulting in a chemically immobilized leuco-dye. The product can be purified in several ways including washing accompanied by centrifugation.

Example with basic fuchsin-sodium sulfite leuco-dye of general formula (I) immobilized on chitosan polymers

Chitosan (1.2 g) was dissolved in 60 mL (2% acetic acid) solution in a 150 mL Erlenmeyer flask equipped with a Teflon-coated magnetic stir bar. The solution was stirred for 30 min at RT followed by addition of basic fuchsin (470 l_, 5.1 x 10 ^-3 mmol) to the light yellow viscous chitosan solution whilst stirring for 30 min further. Acetaldehyde (285 L, 5.1 x 1 O~ ³ mmol) was added to the mixture, and a white low-viscous solution was formed. The reaction mixture was stirred at 70 °C for 18 h. A 3 M NaOH solution was added gradually to the reaction mixture with vigorous stirring and a pH of up to 7 was attained, where a pink precipitate was formed. The precipitate was separated from the supernatant using a centrifuge for 10 min and washed several times with water and ethanol 70%, dried in a vacuum oven at 50 °C for 6 h and stored in a glass vial. IR: v (cm ¹ ) = 3100, 1650, 1480, 1470, 1100, 1050, 920, 800.

General detection of nucleic acids with immobilized leuco-dye

A strip of polymeric material with the immobilized leuco-dye of general formula (I) (strip 1) was brought into contact with solution containing the target nucleic acids. Another strip of polymeric material with immobilized leuco-dye of general formula (I) (strip R) was dipped into a solution without the target nucleic acids as a control. Strip 1 changed its colour indicating the presence of the target nucleic acids in the solution while strip R retained its initial colour.

Example of chemical immobilization of methyl green - sodium sulfite leuco-dye of general formula (I) on cellulose acetate

A white coloured cellulose acetate strip with the immobilized methyl green-sodium sulfite leuco-dye of general formula (I) (strip 1) was brought into contact with a solution containing target nucleic acids. Another white coloured cellulose acetate strip with immobilized methyl green leuco-dye of general formula (I) (strip R) was brought into contact with a solution without the target nucleic acids as a control. Strip 1 changed its colour to blue indicating the presence of target nucleic acids in the solution while strip R remained white coloured.

Example of chemical immobilization of methyl green - sodium sulfite leuco-dye of general formula (I) on polycarboxylate nanobeads and cellulose acetate

To a solution of 2.5% polycarboxylate nanobeads (3 drops) was added the leuco dye (100 uL) and the mixture was allowed to incubate for 1 h. The solution retained its white color while in solution, indicating that the leuco dye had remained intact. After the incubation, the leuco-dye & nanobead mixture was spread on a cellulose acetate membrane and allowed to dry at room temperature for 1 h. Caution should be taken to not allow the nanobeads to dry prior to spreading it onto a cellulose acetate membrane. If the nanobeads are left to dry without spreading on a cellulose acetate membrane (i.e., the cellulose acetate seems important to keep the color intac)t. Subsequently, the nanobead & cellulose acetate membrane is attached to a lateral flow setup and tested for DNA detection.