WO2023001839A2

WO2023001839A2 - A detection kit and methods of detection of infectious agents

Info

Publication number: WO2023001839A2
Application number: PCT/EP2022/070244
Authority: WO
Inventors: Anna GUILDFORD; Sophia KHAN; Flavia BONALUMI; Michela BUONOCORE; Anna Maria D'URSI; Matteo Santin
Original assignee: Tissue Click Limited
Priority date: 2021-07-19
Filing date: 2022-07-19
Publication date: 2023-01-26
Also published as: WO2023001839A3; GB202110391D0

Abstract

The present invention relates to a kit for the antibody-free concentration and detection of specific biomarkers of viral and microbial infection diseases. More specifically, the kit relies on the capture of the infectious agent or its compounds by superparamagnetic nanoparticles functionalised with biomarker-specific peptide aptamers. Magnets enable the concentration of the infectious agent or its fragments in a biological test sample thus enhancing the sensitivity of the detection. The detection is then achieved by the recognition of separate domains of the same or different biomarkers of the infectious agent by different peptide aptamers conjugated with one or more detectable labels, for example fluorophore molecules. The presence of the infectious agent and/or of its fragments may be rapidly detected by the naked eye using a portable illumination apparatus equipped with a fluorescent torch.

Description

A Detection Kit and Methods of Detection of Infectious Agents

The present invention relates to the field of detection of infectious disease agents for the prevention and control of disease, in particular a disease resulting from viral or bacterial infection. In particular, the present invention relates to antibody-free methods of concentration and /or detection of the presence of infectious disease agents and related diagnostic kits.

Viruses and bacteria are the causes of infection in millions of individuals worldwide each year.

They are the cause of outbreaks of infectious disease and present a constant threat of the insurgence of pandemics, which result in severe socio-economical burdens. Infections of zoonotic origin are of particular epidemiological relevance, being estimated to be the cause of 75% of infections in humans. Thus, tracking and tracing of such infections in humans, animals and environmental sources is recognised to be a key action for their control (1). There is therefore a need for sensitive, selective and reliable testing methods that can be easily implemented in the wider population and/or without the requirement for specialised facilities, which is desirable for the control and the eradication of new outbreaks of disease (2). In addition to their sensitivity and selectivity, these tests need to be operator-friendly and not to be dependent on technically sophisticated and expensive equipment. These types of tests may be key in the control of pandemics, such as those caused by viruses, for examples viruses responsible for severe acute respiratory syndromes (SARS), in particular the coronavirus SARS-Cov-2 and its variants (3). For example, lateral flow tests based on the antibody-driven recognition of molecular domains of the infectious disease, referred to herein as biomarkers, have been adopted for the SARS-CoV-2 pandemic at the points of care (4, 5) in conjunction with more laborious yet more sensitive RT-PCR methods in all their most recent developments (6, 7). Although lateral flow tests do not require any equipment to read the results of the tests, they have a relatively low sensitivity when virus concentrations are in the region of or below 10^L7 virus particles/mL and are prone to false negative results (over 40% if used by non-trained operators). In addition, both RT-PCR and lateral flow tests require the application of relatively invasive nasopharyngeal swabs which are unpleasant to repeat frequently and unsuitable to some individuals, which reduces test compliance and makes saliva (also defined as sputum) a more suitable body fluid for SARS testing (8).

Moreover, during RT-PCR and lateral flow tests, the operator is also potentially exposed to the virus during the sample preparation. Many other methods for the detection of infectious diseases in particular of SARS-Cov-2 and its variants, have been described which, similar to the lateral flow test, are based on the recognition of the target biomarker by antibodies (9-12).

Antibody-free detection methods for the detection of SARS-CoV-2 by electrochemical signals generated by enhanced radical oxygen species in sputum have been described (13). Other antibody-free detection methods have been described which include the use of nucleic acid sequences, called aptamers, that are identified by various techniques and used in combination with a solid support such as nanoparticles to capture the target infectious species (14-19).

Peptide aptamers may be identified by computer modelling, but thus far they have not been considered as components in the development of diagnostics for infections (20-23).

There is therefore a need for a kit that can concentrate diluted biological test samples and enable the sensitive, selective and rapid detection of an infectious disease agent without the requirement of specialised equipment. Such a testing kit can be adopted by clinical, points of care, veterinary and environmental settings.

The components, systems, methods, devices, and kits provided herein relate to a novel diagnostic for infectious diseases that can be readily manufactured without the requirement of expensive or technically sophisticated equipment and materials and therefore can be manufactured in a cost- effective manner in non-specialized facilities.

In one aspect the present invention provides a method of detecting the presence of an infectious disease agent or a fragment thereof in a biological test sample, the method comprising the steps of:

(a) incubating the biological test sample with a first peptide aptamer to obtain the first peptide aptamer bound to the infectious disease agent or fragment thereof wherein:

(i) the first peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof; and

(ii) the first peptide aptamer is bonded to the surface of a superparamagnetic nanoparticle; (b) incubating the test sample with a second peptide aptamer to obtain the second peptide aptamer bound to the infectious disease agent or fragment thereof wherein:

(i) the second peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof;

(ii) the second peptide aptamer is conjugated with one or more detectable labels; and iii) the infectious disease agent or fragment thereof is bound to the first peptide aptamer which is bonded to the surface of a superparamagnetic nanoparticle; c) removing unbound second peptide aptamer; and

(d) detecting the presence of the second peptide aptamer bound to the infectious disease agent or fragment thereof in the biological test sample, wherein the infectious disease agent or fragment thereof is bound to the first peptide aptamer which is bonded to the surface of a superparamagnetic nanoparticle, and wherein detection of bound second aptamer indicates the presence of the infectious disease agent or fragment thereof.

It is an advantage of the aspects of the present invention that it provides sensitive, selective and rapid test results from human and animal body fluids (e.g. saliva, nasopharyngeal swab extracts, blood) and environmental samples (e.g. sewage, agricultural and industrial effluents) without the need of sophisticated equipment and specialised facilities and therefore can be adopted, at low cost, in the clinical and field settings as well as at the point of care (POC) to provide rapid POC diagnosis of infection in human, veterinary and environmental samples.

In the context of the present invention, a biological test sample is a test sample which may include an infectious disease agent and includes, but is not limited to, human and animal body fluids (e.g. saliva, nasopharyngeal swab extracts, blood) and environmental samples (e.g. sewage, agricultural and industrial effluents). A skilled person will appreciate that infectious disease agents are organisms that are capable of producing infection or infectious disease. They include bacteria, viruses, fungi, protozoa, and parasites such as helminths.

A skilled person will appreciate that aptamers are oligonucleotide or peptide molecules that bind to a specific target molecule.

More specifically, aptamers can be classified as i) DNA or RNA or XNA aptamers, which consist of (usually short) strands of oligonucleotides; or ii) Peptide aptamers, which consist of one (or more) short variable peptide domains.

Peptide aptamers are artificial proteins selected or engineered to bind specific target molecules. These proteins consist of one or more peptide of variable sequence. They are typically isolated from combinatorial libraries and often subsequently improved by directed mutation or rounds of variable region mutagenesis and selection. Alternatively, they can be obtained by computer models (known as in silico models) which mimic the biospecific recognition properties of natural bioligands (e.g. antibodies).

In the context of the present invention, 'aptamer' is a peptide aptamer.

Magnetic nanoparticles are a class of nanoparticles that can be manipulated using magnetic fields. Such particles commonly consist of two components, a magnetic material, often iron, nickel and cobalt, and a chemical component that has functionality. Nanoparticles are smaller than 1 micrometre in diameter (typically 1-100 nanometres). Superparamagnetism is a form of magnetism which appears in small ferromagnetic or ferrimagnetic nanoparticles. In sufficiently small nanoparticles, magnetization can randomly flip direction under the influence of temperature. The typical time between two flips is called the Neel relaxation time. In the absence of an external magnetic field, when the time used to measure the magnetization of the nanoparticles is much longer than the Neel relaxation time, their magnetization appears to be in average zero; they are said to be in the superparamagnetic state. In this state, an external magnetic field is able to magnetize the nanoparticles, similarly to a paramagnet. However, their magnetic susceptibility is much larger than that of paramagnets.

Peptide aptamers that are covalently coupled to the surface of the superparamagnetic nanoparticle are able to selectively bind to one or more target molecular domains, which act as biomarkers, present on the target infectious disease agent or its fragments. The identification of the peptide sequences of aptamers which are capable of specific recognition of target infectious disease biomarkers may be obtained by in silico methods. In the case of viruses this enables the rapid identification of aptamers which are able to recognize new variants of the infectious agents. The efficiency of coupling of these aptamers to the superparamagnetic nanoparticles and the specific binding to the molecular target may be improved by the introduction of specifically designed molecular spacing arms which maximise the presentation of the aptamer to the molecular target.

Peptide aptamers which are able to selectively bind to one or more target molecular domains, which are biomarkers, present on the target infectious disease agent or fragments thereof and are conjugated to one or more detectable labels are used to detect the presence of the target infectious disease agent. A skilled person will appreciate that the labelling of peptides with detectable labels is well known in the art.

The identification, molecular design and synthesis of peptide aptamers which are able to selectively bind to one or more target molecular domains, which are biomarkers, present on the target infectious disease agent or fragments thereof may include the covalent conjugation with a fluorescent amino acid, the tryptophan, and/or one or more fluorophores (e.g. FITC), which act as detectable fluorescent labels or tags.

Labelling may also be achieved indirectly by using a biotinylated amino acid. If, for example, a biotinylated amino acid is used in peptide synthesis, the biotin group allows specific binding of streptavidin or avidin-conjugate to that site. A variety of fluorophores are available as (strept)avidin conjugates

In one embodiment the or at least one detectable label is a fluorescent tag and the method of detection is detection of a fluorescence signal.

In a further embodiment, the fluorescence signal is in the visible light region of the electromagnetic spectrum such the that fluorescent signal is observable by visual inspection with the naked eye. In one embodiment, the first peptide aptamer that is covalently bonded to the surface of the superparamagnetic nanoparticle specifically binds to one or more target molecular domains of the target infectious disease agent and the second peptide aptamer that is conjugated to one or more detectable labels binds to one or more different target molecular domains of the target infectious disease agent.

A skilled person will appreciate that the first and second peptide aptamers cannot simultaneously bind to same target molecular domain.

In a second aspect the present invention provides a method of increasing the concentration of an infectious disease agent or a fragment thereof in a biological test sample, the method comprising the steps of:

(a') incubating the biological test sample with a peptide aptamer to obtain the peptide aptamer bound to the infectious disease agent or fragment thereof wherein:

(i) the peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof; and

(ii) the peptide aptamer is bonded to the surface of a superparamagnetic nanoparticle; and

(b') applying a magnetic field to the biological test sample, wherein the infectious disease agent or fragment thereof is bound to the aptamer which is bonded to the surface of the superparamagnetic nanoparticle, to generate a concentration gradient in the sample.

Concentration of the infectious disease agent or its fragments in the biological test sample enhances the sensitivity of the detection.

In one embodiment, the present invention provides a method of increasing the concentration of and detecting the presence of an infectious disease agent or a fragment thereof in a biological test sample, the method of claim 1 and claim 2 comprising the steps of:

(a) incubating the biological test sample with a first peptide aptamer to obtain the peptide aptamer bound to the infectious disease agent or fragment thereof wherein: (i) the first peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof; and

(ii) the first peptide aptamer is bonded to the surface of a superparamagnetic nanoparticle;

(b') applying a magnetic field to the biological test sample, wherein the infectious disease agent or fragment thereof is bound to the first peptide aptamer which is bonded to the surface of the superparamagnetic nanoparticle, to generate a concentration gradient in the sample;

(b) incubating the test sample with a second peptide aptamer to obtain the second peptide aptamer bound to the infectious disease agent or fragment thereof wherein:

(d) detecting the presence of the second peptide aptamer bound to the infectious disease agent or fragment thereof in said test sample, wherein the infectious disease agent or fragment thereof is bound to the first peptide aptamer which is bonded to the surface of a superparamagnetic nanoparticle, and wherein detection of bound second aptamer indicates the presence of the infectious disease agent or fragment thereof.

In one embodiment, applying a magnetic field to generate a concentration gradient in the sample results in aggregation of a plurality of the superparamagnetic nanoparticles, optionally to form a multiparticle solid mass or deposit on a surface. In one embodiment, the method as described hereinabove further comprises after step (c) and prior to step (d), the step of adding a dispersant to the sample in the absence of the magnetic field to re-suspend the superparamagnetic nanoparticles in solution; each superparamagnetic nanoparticle is bonded to the first peptide which is bound to the infectious disease agent or fragment thereof and the infectious disease agent or fragment thereof is also bound to the second peptide aptamer; wherein the dispersant optionally comprises a betaine and glucose in aqueous solution.

The use of a dispersant maintains the superparamagnetic nanoparticles in dispersion in an aqueous medium during the detection step (d).

In one embodiment wherein the second peptide aptamer comprises one or more fluorescent tags and the method of detection is detection of a fluorescence signal, detection of fluorescent particulate material, optionally dispersed in aqueous medium, indicates the presence of the infectious disease agent or fragment thereof, .

The present invention further provides a dispersant for suspending nanoparticles in a liquid comprising a betaine, optionally carboxybetaine, and glucose in aqueous solution.

In one embodiment of the methods of the present invention as described hereinabove, the infectious disease agent is selected from viruses, bacteria, fungi and parasites.

In a further embodiment, the infectious disease agent is a virus.

In a yet further embodiment, the virus is a coronavirus, in particular SARS-CoV-2 or a variant thereof.

In a further embodiment wherein the infectious disease agent is a virus, the viral envelope comprises a spike (S) protein, wherein the peptide aptamer has specific binding affinity to one or more molecular domains of the S protein.

In a yet further embodiment, the peptide aptamer has specific binding affinity to one or more molecular domains of the S protein of a coronavirus, in particular SARS-CoV-2 or a variant thereof In a yet further embodiment, the second peptide aptamer is selected from peptide aptamer A and peptide aptamer B, as shown in Figure 5

In a yet further embodiment, the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 1 to Seq ID No. 8, i.e. Seq ID No.s 1, 2, 3, 4, 5, 6, 7 and 8 or combinations thereof .

In a further embodiment wherein the infectious disease agent is a virus, the viral envelope comprises a nucleocapsid (N) protein, wherein the peptide aptamer has specific binding affinity to one or more molecular domains of the N protein.

In a yet further embodiment, the peptide aptamer has specific binding affinity to one or more molecular domains of the N protein of a coronavirus, in particular SARS-CoV-2 or a variant thereof the virus is SARS-CoV-2 or a variant thereof

In a yet further embodiment, the peptide aptamer comprises an amino acid sequence selected from Seq ID No. 9 and Seq ID No. 10, or combination thereof.

In an alternative further embodiment wherein the infectious disease agent is a virus, the virus is feline immunodeficiency virus.

In a yet further embodiment wherein the infectious disease agent is feline immunodeficiency virus, the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 11 to Seq ID No. 19, i.e. Seq ID No.s 11, 12, 13, 14, 15, 16, 17, 18 and 19, or combinations thereof .

In an alternative further embodiment wherein the infectious disease agent is a virus, the virus is human immunodeficiency virus.

In a yet further embodiment, wherein the infectious disease agent is human immunodeficiency virus the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 20 and Seq ID No. 21 and/or from the group consisting of Seq ID No 15 to Seq ID No 19, i.e. Seq ID No.s 15, 16, 17, 18 and 19, or combinations thereof. In a further embodiment, the infectious disease agent is selected from bacteria and fungi.

In a yet further embodiment wherein the infectious disease agent is selected from bacteria and fungi, the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 22 to Seq ID No. 27, i.e. Seq ID No.s 22, 23, 24, 25, 26 and 27, or combinations thereof.

Typically, in the methods of the present invention as described hereinabove, the peptide aptamer comprises an amino acid sequence which is identified in silico as having a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof.

In a further aspect, the present invention provides a diagnostic kit for detecting the presence of an infectious disease agent or a fragment thereof in a biological test sample, the kit comprising

(a) a first peptide aptamer as described hereinabove wherein:

(i) the peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof;

(b) a second peptide aptamer as described hereinabove wherein:

(i) the second peptide aptamer has a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof; and

(ii) the second peptide aptamer is conjugated with one or more detectable labels; c) a container; and d) instructions for use according to the methods of the present invention as described hereinabove. In one embodiment, the kit further comprises a magnet.

In a further embodiment, the kit further comprises a rack equipped with a magnetic base which enables the rapid concentration of the superparamagnetic nanoparticles after each step of the method of the invention as described hereinabove, thus enabling the concentration of the infectious disease agent or fragment thereof which is bound to the aptamer which is bonded to the surface of the superparamagnetic nanoparticle, the efficient incubation steps with the kit reagents, and the removal of unbound second peptide aptamer in a washing step ;

In a further embodiment, the kit further comprises a dispersant as described hereinabove.

An embodiment includes the recommended protocol for the appropriate and safe use of the kit according to the methods of the present invention as described hereinabove.

All steps of the method may be executed with the biological test sample in a sealed glass vial, thereby reducing the risk of infection to the operator.

In a further aspect, the present invention provides an illumination apparatus for detection of a fluorescence signal in the detection step (d) of the method of the present invention as described hereinabove comprising a housing and a source of visible light, wherein the source of visible light is located within the housing, wherein the housing is impenetrable to light, wherein a viewing aperture is located in the housing; and wherein the light source is located below a vial containing the sample, optionally wherein the light source is located 2.5 to 3cm below the vial.

Embodiments also include two types of portable illumination apparatus for the reproducible and high sensitivity illumination of the samples that is necessary to detect the fluorescent signals produced by the presence of the biomarker or by their background coloration in the case of its absence in the sample. The specifications of each of these two types of illumination apparatus include the distance of the Ight source, for example torch, from the vial, the size of the aperture through which the sample is examined, the length of the ocular that facilitates the focussing of the eye for the visual inspection.

An embodiment includes the integration all the components of the kit; the reagents, the washing solution, the dispersant solution, the waste vessel and its ingredients, and the hardware (i.e. coded vial rack integrated with a magnetic plate and two types of portable black boxes for sample illumination).

The skilled person will appreciate that the features described and defined in connection with the aspects of the invention and the embodiments thereof may be combined in any combination, regardless of whether the specific combination is expressly mentioned herein. Thus, all such combinations are considered to be made available to the skilled person.

An embodiment of the invention will now be described, by way of example only, with reference to the accompanying drawings:

Figure 1. A schematic representation of the protocol to execute the test diagnostic.

Figure 1A. A schematic showing use of the magnetic plate and vial holder.

Figure 2. Examples of the two in silico steps to identify peptide aptamers for the selective recognition of infectious disease biomarker. The image is related to the discovery of aptamers for the Protein S of SARS-CoV-2. (A) Preliminary rigid docking, (B) Molecular dynamics simulation.

Figure 3. A schematic representation of the method of functionalization of the surface of superparamagnetic nanoparticles with identified peptide aptamers.

Figure 4. Typical design of (A) the coded magnetic rack and its magnetic base and (B) example of the calculation of the magnetic force necessary to pull the superparamagnetic nanoparticles from volumes of 1 mL and higher of viscous fluids such as saliva.

Figure 5. Molecular structures of fluorophore-tagged aptamers recognising two lateral domains of the SARS-CoV-2 Protein S in proximity of its sub-unit amino terminal. (A) Example of an aptamer including a glycine-glycine spacing arm, a fluorescent tryptophan residue, and an FITC molecule, (B) the same molecule with branching provided by a lysine residue enabling the coupling of two FITC molecules.

Figure 6. Two designs of portable illumination apparatus for reliable sample illumination. (A) Bench top specification, (B) Key holder specification. Figure 7. Typical visual inspection of samples upon illumination in the black box. (A) Negative sample, (B) Positive sample showing fluorescent particles (arrows).

The test comprises a first step (Figure 1) wherein a volume of sample, typically (but not limited to) 1 mL is collected and injected into a 2 mL glass vial, which is sealed with a rubber stopper, using syringe which pierces the stopper with the needle. If present, the infectious agent or its fragments will be rapidly captured by superparamagnetic nanoparticles (typically but not limited to a 50-nm diameter) coated with an inorganic (e.g. silica, SiC>2@MNP) or polymeric (e.g. polyacrylic acid, PAA@MNP) layer and functionalised with a first peptide aptamer, the sequence of which is typically (but not limited to) 5 to 10 amino acid residues and is able to recognize specifically a biomolecule of the infectious disease (e.g. a protein, a glycoprotein, a polysaccharide). The capture of the biomarker will take place in a matter of seconds and completed in no more than 15 min whilst applying an occasional gentle agitation of the nanoparticles to maximise dispersion in the test sample.

The peptide aptamers which are able to specifically recognise the biomarker of the infectious disease agent, are typically identified by computer modelling based on either crystallographic data of the target molecular domain or through that of a natural antibody able to recognise it. The identification of the peptide sequences is conducted in silico in two steps (Figures 2 A and B). Firstly, a preliminary rigid docking is performed which allows the generation of different molecular configurations between ligand and target. A docking score is attributed to each of these configurations which corresponds to the potential energy of the interaction. The sequences which receive the lower docking scores are used for Molecular Dynamics simulations. FI DOCK software is used for identification of the first (capture) peptide aptamer and Glide (Maestro package) is used for identification of the second (detection) peptide aptamer. Molecular dynamics simulations are performed using GROMACS/2020.3 (Force field: CFIARMM).

Docking scores are then redefined after the addition of a spacer arm typically comprising (but not limited to) two residues of glycine to the carboxyl terminal of any of the identified peptide aptamers. These are further assessed for their docking score to the target biomarker after their conjugation to the superparamagnetic nanoparticle such as the SiC>2@MNP.

IB In a typical process for functionalisation of the superparamagnetic nanoparticles with the first peptide aptamer, the peptide is conjugated to the coating surface of the superparamagnetic nanoparticles. For example, the conjugation of the peptide aptamer to Si0₂@MNP may be obtained by mild activation of the oxygen atoms of the silica to generate oxygen radicals which is effected by treatment with a diluted hydrogen peroxide solution, followed by the incubation of the Si0₂@MNP with the peptide aptamer. The latter is previously activated by a well-known succinic anhydride/ethylene diamine reaction in water (Figure 3). The covalent binding of single amino acid can be pursued through the same method prior to the attachment of the aptamer to the purpose of improving the aptamer coupling and subsequent presentation to the biomarker during the test procedure.

For example, the recognition of SARS-CoV-2 virus (i.e. Covid-19) and its variants by the Si0₂@MNP or others is obtained by the in silico identification and solid-phase peptide synthesis of any of the peptide aptamers reported in Table 1. These aptamers which can specifically recognize the Protein S receptor binding domain (RBD) of the virus (Seq ID No. 3 and Seq ID No. 4) mimic a domain of the ACE-2 receptor of the lung cells that is used by the viruses to invade the cells.

Alternatively, aptamer sequences for the Protein S can be obtained from the crystallographic structure of antibodies against the same virus protein (Table 1).

Likewise, peptide aptamers are available that recognize the nucleoprotein of the virus capsid (Table 1).

Peptide aptamers are available that recognize proteins of other viruses such as the human and animal immunodeficiency viruses or those of bacteria and fungi (Table 1, ref. 11-25).

In the second step of the test (Figure 1), the concentration of the captured biomarker is effected by attraction of the aptamer-functionalized superparamagnetic nanoparticles to the bottom of the vial by a purposedly-designed magnetic plate equipped with a coded vial rack able to facilitate the operator with the correct handling and identification of multiple samples (Figure 4 A). The magnetic force necessary to pull the aptamer-functionalized superparamagnetic nanoparticles to the bottom of the vial is calculated to secure their pelleting even when dispersed in viscous biological and environmental samples (Figure 4 B). Concentration is obtained in no more than 5 min of contact with the magnetic plate. The supernatant fluid is then removed by aspiration through a needle piercing the rubber stopper whilst the vial is placed in contact with the magnetic plate to avoid the loss of the nanoparticles. This is immediately disposed in a safe manner in a vial containing a lytic solution able to destroy viruses and bacteria.

The aptamer-functionalized superparamagnetic nanoparticles that have captured the infectious disease agent (e.g. SARS-CoV-2 virus or its fragments) are then rapidly washed with a small volume (e.g. 0.1 mL) of deionised water by removal of the vial from the magnetic plate, gentle agitation to resuspend the nanoparticles and their collection to the bottom of the vial by no longer than 3 min placing of the vial on the magnetic plate. Two washing steps are typically performed to secure complete washing from the excess of unbound and unwanted sample components. To avoid loss of nanoparticles, washings are performed by adding and removing the liquid volume when the vial is located on the magnetic plate. Only a rapid and gentle agitation away from the magnetic plate is required to achieve a thorough washing.

In the third step (Figure 1), a small volume (typically 0.03 mL) of a solution (typically but not limited to O.lmg/mL aptamer in deionised water) of peptide aptamers able to recognize one or more different domains of the same biomarker (e.g. Protein S) is added. These aptamers, identified by the above described in silico methods (Table 1), are synthesized to bear a fluorescent amino acid (i.e. tryptophan) as well as one or more molecules of a fluorophore (e.g. FITC) (Figures 5 A and B). The coupling with tryptophan as well as with the fluorophore is obtained at the amino-terminal of the peptide sequence by a well-known coupling method. The coupling with two molecules of fluorophore is obtained by adding a molecule of lysine that makes available two amino terminals to the fluorophore covalent grafting. After 5 minutes of incubation, the solution of the fluorophore-tagged peptide aptamers is removed by a syringe after attracting the aptamer- functionalized superparamagnetic nanoparticles to the bottom of the vial by the magnetic plate as described above. At this stage and if present, the biomarker will be bound to both the superparamagnetic nanoparticles and to one (or more) aptamer(s) recognizing one (or more) of its other domain(s).

Two washing steps are then performed as described above.

A small volume of a dispersant solution is then added to re-suspend the superparamagnetic nanoparticles. The dispersant solution is made of carboxybetaine (e.g. 100 mg/mL) and glucose (e.g. 0.01% w/vol) dissolved in distilled water or any other buffer. After gentle agitation, the vial is positioned in a portable illumination apparatus of the specification required to keep the bottom of the vial at a typical distance of 2.5cm (or as appropriate depending on the light source and vial specifications) from the light source and with an ocular aperture enabling the focussing of the eye during the visual inspection of the sample (Figures 6 A and B).

A negative test yields lack of fluorescence as shown in Figure 7 A. A positive detection of the infectious agent biomarker is determined by the observation of fluorescent particles as shown in Figure 7 B, arrows. The fluorescence develops immediately and provides reliable reading within 15 minutes from addition of the dispersant solution. In the case of SARS-Cov-2 testing, Protein S amounts typically ranging from 300 femtograms to 3.0 micrograms and beyond can be reliably detected.

Examples

A further definition of the embodiments of the present invention is provided through the following Examples. These Examples are given only as an illustration of the typical use of the kit and its components in a way that ensures the most reliable outcome of the test and they are not intended to limit its use to the specific infectious disease here reported, i.e. the testing of human saliva for the detection of SARS-Cov-2 Protein S. Depending on the samples to be analysed and the setting in which the kit will be used, a skilled operator will understand that some of the embodiments of this invention may require adaptations. These changes will be obvious to such an operator reading the descriptions hereinafter reported. Any of these modifications are also intended to fall within the scope of the claims of this invention.

Example 1 Sample collection

A volume of saliva of approximately 1 mL is collected in a vessel of a shape and size that makes the sample collection easy and that ensures its sealing with a screw cap. A 2-mL plastic syringe is then used. The needle is removed from the syringe and used to pierce the rubber stopper of the kit sealed glass vial containing a suspension of silica coated magnetic nanoparticles (Si0₂@MNP) functionalised with the aptamer Seq. ID No. 1 that specifically bind the RBD of the Protein S. A few piercings of the rubber stopper are recommended to avoid air back pressure at the time of the saliva injection. The 2-mL plastic syringe without the needle is then used to aspirate circa 1 mL of saliva from the collection vessel. The syringe is then connected to the needle without removing the latter from the rubber stopper. A gentle tilting of the needle allows the release of air from the vial further avoiding risks of back pressure upon injection of the sample into the vial. This operation is then performed by applying a gentle and continuous pressure on the syringe plunge.

Example 2 Sample Incubation

The vial rack is removed from the magnetic base and located on a flat bench surface far from the magnet base. The vial(s), previously labelled according to the coding system adopted by the operator, is (are) positioned in the separated rack after gentle, manual agitation to guarantee the thorough distribution of the aptamer-functionalised Si0₂@MNP within the saliva sample. The capture of the virus or its Protein S fragments is maximized by an incubation of 15 min during which each vial is occasionally agitated to maintain the aptamer-functionalised Si0₂@MNP in suspension. The incubation can exceed the 15 min.

Example 3

Sample removal and washing of the superparamagnetic nanoparticles After the 15 min (or longer) incubation, the rack containing the vial(s) is positioned on its magnetic base and left for 5 min to ensure the pulling of the aptamer-functionalised Si0₂@MNP to the bottom of the vial. Keeping the vial in contact with the magnetic plate, the saliva is aspirated taking precaution that the nanoparticles remain adhering on the bottom of the vial. This is usually obtained by positioning the tip of the needle close to the centre of the vials while the magnetic force distribute the nanoparticles at the periphery. The contaminated syringe and needles are then removed and disposed safely according to the health and safety procedure of the setting in which the test is performed. The rack is then detached from the magnetic base. Using a clean needle and syringe, 1.5 mL of deioinized water is then added to the vial and its content resuspended by a gentle agitation. The rack is returned to its magnetic base to attract the aptamer-functionalised Si0₂@MNP to the vial bottom, the supernatant is removed and the washing procedure is repeated at least once more following the same procedure and removing the supernatant of the last water wash. All supernatants need to be disposed of by injection into the disposal bottle containing the lytic solution.

Example 4

Incubation of the aptamer-functionalised SiO_?(5⁾MNP with fluorophore-tagged aptamer(s)

The aptamer-functionalised Si0₂@MNP are then incubated for 5 minutes with 0.03 mL (ca 3 droplets released by the plastic syringe) of the 0.1 mg/mL solution of the two aptamers Seq ID No. 2 and Seq ID No. 3 the powder of which is reconstituted in deionized water immediately before its use. The injection of these FITC-tagged aptamers is performed with a clean syringe and needle. After 5 minutes of incubation, the FITC-tagged aptamer solution is removed and the content of the vial is washed twice as described above. In all steps, it is important to make sure that no residual liquid is left in the needle. After the washing steps are completed, the last washing supernatant needs to be removed and disposed of in a safe manner into the lytic solution as described in Example 3.

Example 5 Rapid test

A method of a rapid analysis where the saliva samples collected as reported in Example 1 are simultaneously incubated with the aptamer-functionalised Si0₂@MNP of Example 2 and with the fluorophore-tagged aptamer of Example 3 and with the use of plastic pipettes rather than needles whereby the test then performed through the following steps:

• Test vial preparation

1. Remove the vial holder from the magnetic plate and place it about 50 cm away from it (Figure 1A)

2. Label each vial to uniquely link it to the corresponding patient and put it into the vial holder

3. Remove the seal from each test vial being used (containing aptamer-functionalised Si0₂@MNP).

4. Take a plastic pipette and reconstitute Vial A ( containing the fluorophore-tagged aptamer - 1 vial will complete 10 tests) by adding 1ml of distilled water. Shake the vials to allow mixing

5. Using the same pipette add 10 drop of solution A to each test vial (discard the pipette and vial once empty)

• Sample preparation

1. Using a new pipette for each sample, transfer about 1 ml of saliva into the test vial.

2. Discard the pipette into the appropriate waste bin

3. Pick the test vial and tap with the finger to ensure particle resuspension and thorough mixing (Never put the vial upside down) 4. Return the test vial to the holder and leave it to react for 5 minutes • Performing the test

1. Place the vial holder containing the test vial on the magnetic plate for 3 minutes

2. With a new pipette for each vial, remove the liquid from the centre of the test vial and discard liquid in the waste bottle with the SDS solution and dispose of the pipette.

3. Remove the vial holder from the magnetic plate and place it about 50 cm away from it

4. With a new pipette, add an excess of water to the test vial

5. Place the vial holder containing the test vial on the magnetic plate for 30 seconds

6. With the same pipette, remove the liquid from the centre of the vial and discard liquid in the waste bottle with the SDS solution and dispose of the pipette

7. Remove the vial holder from the magnetic plate and place it about 50 cm away from it

8. Remove the seal from the vial labelled B (containing a dispersant solution)

9. With a new pipette, add 10 drops to the test vial.

And where the reading of the results is performed as reported in Example 6.

Example 6 Sample analysis

After the washing steps and removal of the last supernatant, the rack is removed from the magnetic base and ca 0.150 mL of dispersant solution are added to each vial. After a gentle agitation to resuspend its content, the reading of the test can be taken within 15 min by positioning the vial in the illumination apparatus where the optimal illumination is achieved by the location of the torch at the bottom of the vial and at a distance ranging from 2.5 cm to 3 cm. The fluorescent staining appears almost immediately in SARS-Cov-2-positive samples, but an optimal reading can be observed in the time range of 5 to 10 min. The result of the test is obtained by visual inspection through a slot and it can be documented by any digital camera as those of mobile devices or reported following any other system adopted at the testing site. Reliable positive tests can be obtained in a range of Protein S amount ranging from 300.0 femtograms to 3.0 micrograms in the form of resuspended fluorescent particles.

Example 7 Clinical Trial Data

Clinical trials have been completed using the TC19 test kit. 359 participants were included in the multicentre clinical trials. The ages of the participants ranged from 4 to 93 years of age, 9% of participants were under 18, 78% were between the ages of 18-65 and 7% were 65+, the ages of the remainder are unknown. 57% of participants were male. TC19 test kit was measured for sensitivity and selectivity against the gold standard PCR. It has demonstrated 98% selectivity for the SARS-CoV-2 virus when assessed against PCR and 95% sensitivity.

Table 1

Target Infectious Target Biomarker Specific Aptamers Ranked Binding Affinity Agent (kcal/mol)

Typical Viral Agents

Seq ID No.l TFLDK Coulomb-SR: -194.759;

Protein S LJ-SR: -116.825

Receptor Binding

Seq ID No.2 DKFNH Coulomb-SR: -246.606; Motif LJ-SR: -89.2601

Seq ID No.3 SEYDPYY Coulomb-SR: -129.544;

Protein S LJ-SR: -154.802 Receptor Binding

SARS-CoV-2 (Covid- Seq ID No. 4 NFWPY Coulomb-SR: -150.439;

Domain

19) and variants LJ-SR: -76.6983

Seq ID No. 5 GYTLTE Coulomb-SR: -384.989; LJ-SR: -142.701

Protein S Amino Seq ID No. 6 TGEAAEY Coulomb-SR: -326.504; Terminal LJ-SR: -101.831

Seq ID No. 7 VAGTPDLF Coulomb-SR: -256.388; LJ-SR: -141.180 Seq ID No. 8 VTPDF Coulomb-SR: -248.867;

LJ-SR: -46.799

Seq ID No. 9 QSGHSNYA Coulomb-SR: -351.25;

Nucleocapsid LJ-SR: -147.692 Amino Terminal Coulomb-SR: -313.651;

Seq ID No. 10 YETDGDYS

LJ-SR: -114.548

FIV (Feline gp36 membrane Seq ID No. 11 WEDWVGWI n/a Immunodeficiency proximal external Seq ID No.12 WEDWVG n/a virus) (20, 21) region (M PER) Seq ID No. 13 DWVGWI n/a Seq ID No 14 EDWVR n/a

Also suitable for

Seq ID 15 QYHQV n/a

HIV

Also suitable for

Seq ID 16 LATHQ n/a

HIV

Also suitable for

Seq ID 17 LYTAFA n/a

HIV

Also suitable for

Seq ID 18 NQTIW n/a

HIV

Also suitable for

Seq ID 19 NHGNI

HIV

HIV (Human gp41 membrane Seq ID No.20 DFWSGYP n/a Immunodeficiency proximal external

Seq ID No. 21 DNAW n/a virus) (20, 21) region (MPER)

Seq ID No. 22 RRWWRF n/a Seq ID No. 23 cyclo- n/a RRWWRF

Seq ID No. 24 HRRWWRF n/a

Bacteria and Fungi Seq ID No. 25 cyclo- n/a (22, 23) HRRWWRF

Seq ID No. 26 n/a

HGHRRWWRF

Seq ID No. 27 cyclo- n/a

HGHRRWWRF References

(1) Control of neglected zoonotic diseases: challenges and the way forward (2005) https://www.who.int/zoonoses/Consultation_Sept05_en.pdf

(2) Kost GJ. Geospatial Hotspots Need Point-of-Care Strategies to Stop Highly Infectious Outbreaks. Arch Pathol Lab Med 2020; 144(10): 1166-1190

(3) Cheng MP, Papenburg J, Desjardins M, Kanjilal S, Quach C, Libman M, Dittrich S, Yansouni CP. Diagnostic Testing for Severe Acute Respiratory Syndrome-Related Coronavirus 2: A Narrative Review. Ann Intern Med, 2020; 172(11): 726-734. doi: 10.7326/M20-1301.

(4) WO 2021/007249 A1

(5) PCT/US2020/041067

(6) WO 2020/245808 A1

(7) PCT/IB2020/055348

(8) Khurshid Z, Asiri FYI, Al Wadaani H. Human Saliva: Non-lnvasive Fluid for Detecting Novel Coronavirus (2019-nCoV). Int J Environ Res Public Health, 2020; 17(7): 2225. doi: 10.3390/ijerphl7072225

(9) PCT/US2014/060429

(10)US 10,948,490 B1

(11)US 10,975,139 B1

(12)EP 3809 137 Al

(13)US 2020/0340945

(14)WO 2007/117444 A2

(15)US 10,883,149 B2

(16)US 2009/0291508 Al

(17)US 2013/0137090 Al

(18)WO 2019/117518 Al

(19)US 9,891,227 B2

(20)Giannecchini S, Di Fenza A, D'Ursi AM, Matteucci D, Rovero P, Bendinelli M: Antiviral Activity and Conformational Features of an Octapeptide Derived from the Membrane- Proximal Ectodomain of the Feline Immunodeficiency Virus Transmembrane Glycoprotein. J Virol 2003; 77(6): 3724-3733; DOI: 10.1128/JVI.77.6.3724-3733.2003 (21)Grimaldi M, Stillitano I, Amodio G, Santoro A, Buonocore M, Moltedo O, Remondelli P, D'Ursi AM: Structural basis of antiviral activity of peptides from MPER of FIV gp36. PLoS ONE 2018, 13(9): e0204042

(22)Grimaldi M, De Rosa M, Di Marino S, Scrima M, Posteraro B, Sanguinetti M, Fadda G, Soriente A, D'Ursi AM, Synthesis of new antifungal peptides selective against Cryptococcus neoformans. Bioorg Med Chem, 2010; 18(22): 7985-7990, ISSN 0968-0896, https://doi.Org/10.1016/j.bmc.2010.09.033.

(23)Di Marino S, Scrima M, Grimaldi M, D'Errico G, Vitiello G, Sanguinetti M, De Rosa M, Soriente A, Novellino E, D'Ursi AM, Antifungal peptides at membrane interaction, Eur J Med Chem, 2012; 51: 154-162, ISSN 0223-5234, https://doi.Org/10.1016/j.ejmech.2012.02.037.

Claims

1. A method of detecting the presence of an infectious disease agent or a fragment thereof in a biological test sample, the method comprising the steps of:

2. A method of increasing the concentration of an infectious disease agent or a fragment thereof in a biological test sample, the method comprising the steps of: (a') incubating the biological test sample with a peptide aptamer to obtain the peptide aptamer bound to the infectious disease agent or fragment thereof wherein:

3. The method of claim 1 or claim 2 comprising the steps of:

(d) detecting the presence of the second peptide aptamer bound to the infectious disease agent or fragment thereof in said test sample wherein the infectious disease agent or fragment thereof is bound to the first peptide aptamer which is bonded to the surface of a superparamagnetic nanoparticle, and, wherein detection of bound second aptamer indicates the presence of the infectious disease agent or fragment thereof.

4. The method of claim 1 or 3 wherein the or at least one detectable label is a fluorescent tag and the method of detection is detection of a fluorescence signal, optionally wherein the fluorescence signal is in the visible light region of the electromagnetic spectrum.

5. The method of any of claims 2 to 4 wherein in step (b'), applying a magnetic field to generate a concentration gradient in the sample results in aggregation of a plurality of the superparamagnetic nanoparticles, optionally to form a multiparticle solid mass or deposit on a surface.

6. The method of any of claims 3 to 5 wherein the method further comprises after step (c) and prior to step (d), the step of adding a dispersant to the sample in the absence of the magnetic field to re-suspend the superparamagnetic nanoparticles in solution; each superparamagnetic particle is bonded to the first peptide which bound to the infectious disease agent or fragment thereof, and the infectious disease agent or fragment thereof is also bound to the second peptide aptamer; wherein the dispersant optionally comprises a betaine and glucose in aqueous solution.

7. The method of any of claims 1 to 6 wherein the infectious disease agent is selected from viruses, bacteria, fungi and parasites.

8. The method of claim 7 when the infectious disease agent is a virus.

9. The method of claim 8 wherein the virus is a coronavirus.

10. The method of claim 9 wherein the coronavirus is SARS-CoV-2 or a variant thereof.

11. The method of any of claims 8 to 10 wherein the viral envelope comprises a spike (S) protein, wherein the peptide aptamer has specific binding affinity to one or more molecular domains of the S protein.

12 The method of claim 11 wherein the virus is SARS-CoV-2 or a variant thereof

13. The method of claim 12 wherein the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 1 to Seq ID No. 8.

14 The method of any of claims 8 to 10 wherein the viral envelope comprises a nucleocapsid (N) protein, wherein the peptide aptamer has specific binding affinity to one or more molecular domains of the N protein.

15. The method of claim 14 wherein the virus is SARS-CoV-2 or a variant thereof

16. The method of claim 15 wherein the peptide aptamer comprises an amino acid sequence selected from Seq ID No. 9 and Seq ID No. 10.

17. The method of claim 16 wherein the virus is feline immunodeficiency virus.

18. The method of claim 17 wherein the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 11 to Seq ID No. 19.

19. The method of claim 8 wherein the virus is human immunodeficiency virus.

20. The method of claim 19 wherein the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 20 and Seq ID No. 21 and/or from the group consisting of Seq ID No 15 to Seq ID No 19.

21. The method of claim 7 wherein the infectious disease agent is selected from bacteria and fungi.

22. The method of claim 21 wherein the peptide aptamer comprises an amino acid sequence selected from the group consisting of Seq ID No. 22 to Seq ID No. 27.

23. The method as claimed in any preceding claim wherein the peptide aptamer comprises an amino acid sequence which is identified in silico as having a specific binding affinity to one or more molecular domains of the infectious disease agent or a fragment thereof

24. A diagnostic kit for detecting the presence of an infectious disease agent or a fragment thereof in a biological test sample, the kit comprising

(a) a first peptide aptamer according to any preceding claim wherein:

(b) a second peptide aptamer according to any preceding claim wherein:

(ii) the second peptide aptamer is conjugated with one or more detectable labels; c) a container; and d) instructions for use according to the method of any preceding claim.

25. A kit as claimed in claim 24 which further comprises a magnet.

26. A dispersant for suspending nanoparticles in a liquid comprising a betaine, optionally carboxybetaine, and glucose in aqueous solution.

27. A kit as claimed in claim 24 or 25 which further comprises a dispersant according to claim 26.

28. An illumination apparatus for detection of a fluorescence signal in the detection step of the method of any of claims 1 and 3 to 23 comprising a housing and a source of visible light, wherein the source of visible light is located within the housing, wherein the housing is impenetrable to light, wherein a viewing aperture is located in the housing; and wherein the light source is located below a vial containing the sample, optionally wherein the light source is located 2.5 to 3cm below the vial.