WO2022049493A1

WO2022049493A1 - Diagnostic methods for cov2 antigen detection in normal healthy asymptomatic and symptomatic patients at home or at point of care

Info

Publication number: WO2022049493A1
Application number: PCT/IB2021/057971
Authority: WO
Inventors: Uday Saxena; Satishchandran CHANDRASEKHAR; Gopi KADIYALA; Subramanian Iyer; Subrahmanyam VANGALA
Original assignee: Reagene Innovations Pvt. Ltd.
Priority date: 2020-09-04
Filing date: 2021-09-01
Publication date: 2022-03-10

Abstract

The technology described in this application is designed to detect the SARS-CoV-2 N-protein in bodily fluids (saliva, nasal/oral swabs, serum, blood) by methods using chicken IgY antibodies, monoclonal IgGs, polycolonal IgGs, camelid nanobodies, phage display derived binding proteins etc. raised separately against two domains of the N-protein separately in order to provide for additional sensitivity and specificity, and without interference through competition by the capture and detector antibodies.

Description

Diagnostic methods for CoV2 antigen detection in normal healthy asymptomatic and symptomatic patients at home or at point of care

RELATED APPLICATION

This application is related to and takes priority from Indian Application No. 202041038265 filed 4^th September 2020 (4/9/2020) and is incorporated herein in its entirety.

FIELD OF INVENTION

The present invention provides assays for detection of COVID- 19 in normal healthy asymptomatic and symptomatic patients.

BACKGROUND OF INVENTION

COVID-19 has created havoc globally both with its mortality and its debilitating effects seen in patients. Previously it was thought that the viral infection mostly impairs lung cells, but now it has been shown in patients that other cell/tissues/organs such as endothelium, kidney and heart are also majorly impacted. Importantly, abnormal blood clotting and inflammation are being now thought as important causes of the damage caused by the viral infections.

There are several assay kits available in the market for the detection of Covid- 19 virus. While some of these are for the detection of RNA and antibodies, there are others which are for the detection of Covid-19 specific protein antigens. Amongst those for the detection of antigens, few are available for the detection of the Nucleocapsid (N) protein (as given in the table below).

Some of these (Beijing Kewei Clinical, SD BIOSENSOR, Inc, Shenzhen Bioeasy Biotechnology Co., Ltd) however are fluorescence based and need additional infrastructure, while the others (Bionote Inc., Confirm BioSciences, SD BIOSENSOR, Inc.) show SARS reactivity as well.

SUMMARY OF INVENTION

The technology described in this application is designed to detect the SARS-CoV-2 N-protein in bodily fluids (saliva, nasal/oral swabs, serum, blood) by methods using chicken IgY antibodies, monoclonal IgGs, polycolonal IgGs, camelid nanobodies, phage display derived binding proteins etc. raised separately against two domains of the N-protein separately in order to provide for additional sensitivity and specificity, and without interference through competition by the capture and detector antibodies. These assays may be conducted in various formats such as lateral flow, direct and indirect ELISA, dot blot, fast flow etc. Anti-domain 1 and anti-domain 2 may be switched to accommodate one as the capture and the other as the detector antibody.

BRIEF DESCRIPTION OF DRAWINGS

Figure 1. Crystal structure of SARS CoV N-protein used for domain selection.

Figure 2. Structure of CoV2 N-protein N and C terminal domains of the invention and its interactions.

Figure 3. Structural Organization of SARS-CoV-2 N protein and sequence alignment.

Figure 4. Concept of antigen-antibody reaction a) antigen-antibody b) IgY -antigen

Figure 5. Schematic representation of LFA design and functionality.

Figure 6. Titer of anti-N1 and anti-N2 IgY

Figure 7. Detection of full length N-protein in LFA. (A) LFA using anti-N2 and anti-N1 combination. (B) LFA using anti-N2 and anti-N2 pair for capture and detection respectively. Figure 8. Detection of full length N-protein in LFA developed using anti-N2 IgY and anti-N-mouse monoclonal IgG antibodies. The LOD is found to be up to Ing/mL.

Figure 9. Dot blot analysis for detection of either N1 or N2 antigens using respective N1 or N2 anti-IgY for capture and detection (detection at 10 μg/ml and 1 μg/ml of antigen).

Figure 10. Dot blot analysis for detection of either N1 or N2 antigens using respective N1 or N2 anti-IgY for capture and detection (detection at 0.25 μg/ml of antigen).

Figure 11. Detection of full-length N protein using an N2 capture and detection by dot blot analysis.

Figure 12. LFA kits tested with COVID- 19 positive saliva samples. (C) Showing control line with nonspecific IgY conjugated with gold nanoparticles bound to anti-IgY captured on the membrane. (T) Test line represents and confirms the sample as positive for COVID- 19 infection.

DETAILED DESCRIPTION OF INVENTION

The technology described in this application is designed to detect the N protein in bodily fluids (saliva, nasal/oral swabs, serum, blood, plasma, sweat) by methods using chicken IgY antibodies, monoclonal IgGs, polycolonal IgGs, camelid nanobodies, phage display derived binding proteins etc raised separately against two domains of the N protein separately in order to provide for additional sensitivity and specificity, and without interference through competition by the capture and detector antibodies. These assays may be conducted in various formats such as lateral flow, direct and indirect ELISA, dot blot, fast flow etc. Anti-domain 1 antibodies and anti-domain 2 antibodies may be switched to accommodate one as the capture and the other as the detector antibody.

The present invention provides an assay method for detection of an antigen using patient nasal or oral swabs or serum or blood or other body fluids. In one embodiment, the invention provides detection of nucleocapsid (N) protein antigen of SARS2-Cov-19 virus.

N protein is the most abundant protein in SARS2-CoV 19 virus and thus the detection sensitivity and selectivity is superior to the detection of spike protein. The present invention is unique in that it provides two separate domains of the N protein antigens: 1) domain 1 as capture antigen; and 2) domain 2 as detection antigen as shown in SEQ ID NO. 1. The protein sequences domain 1 and domain 2 were separately expressed and purified and used as antigens to generate anti-domain 1 and anti-domain 2 antibodies, as shown in SEQ ID NO. 2 and SEQ ID NO. 3.

The basic concepts are outlined in Figure 4.

The potential signal amplification using N protein as antigen is based on the following concept:

• One virion has 1,000 N protein molecules. The assumption here is that the N protein in the virus is complexed to polyclonal antibodies against Domain-2 of N that have been labeled with gold, biotin, HRP (horse radish peroxidase), fluorescent molecule or any other detection method.

• Based on previous work with Dengue virus avians recognize 50 epitopes of its envelope protein as opposed to 5 epitopes recognized by mammals. Using the same extrapolation one N protein would have 50 IgY molecules bound to one N protein)

• Each of the N protein molecules with bound labeled IgY against Domain 2 of N protein is available for signal development

• Anti-Domain 1 IgY is used for immobilization

• Immobilization is efficient at the signal band because anti-N-Domain 1 is also polyclonal IgY, but against Domain- 1 of N protein

• So, if there are only 104 viral particles in a swab, the signal strength would be contributed by

~5x10⁸ anti- Domain 2 antibodies which are utilized for detection

• This level of sensitivity compares well with the current antibody kits and PCR sensitivities.

In another embodiment the structure of SARS CoV-2 N protein used for antigen domains is provided in Figure. 2 (Ref: Antiviral Res. 2014 Mar; 103: 39-50).

In yet another embodiment, the chicken IgY polyclonal antibodies will be raised to both the domains for use in LFA. • It is iterated that the design features shown here for N-protein may be extended to other abundant proteins such as the S protein, and two self-folding domains used antigens for domain 1 and domain 2.

• The N protein is selected by the inventors as it has minimal cross reactivity with other Corona viruses (Structural analysis of B cell epitopes in antibody: protein complexes. Mol Immunology, Elsevier Ltd; 2013, 53: 24-34)

• In another embodiment IgY against Domain 1 alone may be used for both capture and detection or anti-Domain 2 alone may be used for both capture and detection.

• In a further embodiment, any antibody (monoclonal and polyclonal IgG from mammalian sources or nanobodies or Fab fragment derived from phage display) may be substituted for IgY.

In the above provided N protein sequence of SEQ ID NO. 1, domain 1 and domain 2 are differentiated by bolded (domain 2) and italics (domain 1) letters.

SEQ ID NO. 2 (225 aa): N Protein Domain 1

Poly serine-glycine linker and poly histidine at the C-terminal end are bolded. Polyhistidine is included to facilitate purification on nickel columns. A plasmid construct as designed above were used to express the proteins as designed. Purified proteins were used to vaccinate chickens and IgY antibodies isolated from vaccinated chicken eggs.

Chicken vaccination and isolation of IgY were as described in

Poly serine-glycine linker and poly histidine at the C-terminal end are bolded. Polyhistidine is included to facilitate purification on nickel columns.

A plasmid construct as designed above was used to express the proteins as designed. Purified proteins were used to vaccinate chickens and IgY antibodies isolated from vaccinated chicken eggs. Chicken vaccination and isolation of IgY were as described in

The crystal structure of SARS CoV N protein used for domain selection is provided in Figure 1 (J.Vir. 80:13 6612-6620; bioRxiv preprint doi:

The structure of CoV2 N protein N and C terminal domains of the invention and its interactions are provided in Figure 2 (Ref: BBRC, 527:3, 618-623, June 30, 2020).

Structural Organization of SARS-CoV-2 N protein and sequence alignment is shown in Figure 3. Domain structure of SARS-CoV-2 N protein. The domain boundaries are shown on the top and the different domains were labeled in different colors. The predicted structure of SARS-CoV-2 N protein was presented. The NTD and CTD are highlighted.

Figure 4 outlines the concept for an antigen- antibody reaction. A singular polypeptide (Antigen X) is shown schematically having two domains. The two domains of an antigen are selected, and each domain is at least 25 amino acids, preferably a self-folded as in the native protein structure. These protein/peptides are used to immunize or identify antibody - monoclonal, polyclonal IgY, IgG, camelid nanobodies, protein, peptide or mimetics that bind to the domain specifically. The concept can be applied to various formats for detection and quantitation depending on the detection mechanism used. In one embodiment, to detect an antigen in the sample a specific binding/complexing agent to one domain of the antigen is immobilized to the matrix. The sample is applied directly or by flow to bind to the binding/complexing agent resulting in immobilized antigen (complex 1). Addition of the domain 2 specific labeled antibody/complexing agent will bind to domain 2 of the antigen and form a super complex, and the label allows for detection and quantitation of the super complex.

In another embodiment, the capture antibody is IgY and detector antibody labeled is to the same domain of the antigen and this secondary antibody can be IgY, IgG, camelid nanobody or Fab fragment, mimetic etc.

Table 1: Concept of using two domains of N protein in LFA

CONCEPT OF USING TWO DOMAINS OF N-PROTEIN IN LFA

Note: * Gold or other detection module conjugate

$ Biotin labeled

• Target protein is N= 419 aa

• 240 aa at the N-terminal domain of N protein is Domain- Ifor raising polyclonal IgY

• 179 aa at the C-terminal domain of N-protein is Domain-2 for raising polyclonal IgY

• Both IgYs i.e. anti-domain 1 and anti-domain2 are binding to whole N protein

The schematic illustration of the LFA design and functionality is provided in the Figure 5. The step-wise process of the design is provided below:

• Nucleocapsid (NC) protein has a 2-domain structure, an N-terminal domain and C-terminal domain.

• The two domains of the NC protein; N-terminal (NC-N) and C-terminal (NC-C) are separately synthesised.

• These two peptides are used for raising antibodies in chickens, mammals, camels or identified through F(ab) page display. • Binding peptides, proteins or antibodies are isolated. IgY shown in Figure 5 is an example.

• The two purified polyclonal IgYs from chicken egg yolk are anti-NC-N IgY (Yl) and anti-NC-C IgY (Y2).

• Y2 is gold or biotin labelled polyclonal antibody

• Yl is capture polyclonal unlabelled antibody

• The polyclonal Y2 will bind to the C-terminal domain of N protein from the sample to form a complex NC-Y2

• The complex NC-Y2 will then migrate towards the left on the reaction membrane towards absorbent pad

• At the test window the NC-Y2 complex will be captured by Yl by binding to the N-terminal portion of the NC protein and will become visible due to the gold conjugate

• Similarly the non-specific IgY conjugated to gold nanoparticle will migrate from the conjugate pad towards left and bind to anti-IgY captured in the control line and become visible which conforms the assay suitability.

The anti N protein IgY to the two domains of the N protein shown here has high affinity binding to the antigen as shown by the ELISA, LFA and dot blot. This binding of the IgY, Fab’s from phage display or nanobodies could be used for diagnosis of SarsCov2 as claimed but the use could be extended for a diagnostic or a therapeutic as the antibodies may inhibit the functions of viral N protein in COVID 19. Similarly, radiolabeled IgY, Fab’s from phage display or nanobodies from camelid antibodies may be injected into patients and could be used to track the tissue accumulation of the virus such as the lung through imaging techniques used for diagnosis of pathology and treatment such as, X-Ray or gamma ray imaging for whole body scans (PET), or more organ (lung, heart, kidney) and tissue- specific scans (SPECT). Thus the present invention also highlights the use of raising antibodies against two domains of the same antigen as a theranostic (diagnostic and therapeutic) as well as imaging antibodies.

The following Examples further illustrate and enable the method of the invention. These Examples are for illustrative purposes only and do not in any way limit the scope of the invention.

EXAMPLES

Example 1: Development of anti-N1 and anti-N2 IgY

N1 and N2 domain polypeptides of SARS CoV-2 N protein (seq ID 2 and 3 respectively, were used to vaccinate chickens separately and boosted several times with the respective antigens to achieve high titer. Titer was determined using partially (>85%) purified total IgYs from yolk. The ELISA data is shown below. ELISA was carried out as per standard protocol. N1 (lug) or N2 (lug) proteins were coated on the plate (in wells A1 through B9 with N1 and C1 through D9 with N2) overnight. Anti-N1 or anti-N2 as appropriate were diluted as shown and applied to the plate to bind either the N1 protein or the N2 protein.

PC = positive control where a known antigen X was coated on the plate and anti-X-IgY was applied to bind to antigen X.

CPC= Only anti-N1 or anti-N2 or anti-X antibodies were applied. No antigen.

NC = Antigen X was coated on the plate and anti-N1 or anti-N2 IgY antibodies are applied to check if there is any cross reactivity.

The plate was blocked and washed following each addition as per standard ELISA protocol.

The color was developed by complexing HRP conjugated anti- IgY antibody and HRP standard as per standard ELISA protocols.

The results demonstrate that high titer IgY antibodies (>160,000) are obtained against both N1 and N2 peptides (Figure 6) Ability to get high titer antibodies is prerequisite to the development of a sensitive diagnostic assay.

Table 2: Titer of anti-N1 and anti-N2 IgY

Example 2. Sandwich ELISA - Effect of lysis buffer on the sensitivity of detection of N protein

This example utilized a sandwich ELISA in which the antigen is sandwiched between 2 antibodies as depicted in the Concept “A” shown in Figure 4. In this example, the plate is coated with either anti-N1 IgY or anti-N2 IgY as capture antibody and allowed to sit overnight. Full length N protein diluted either in PBS or lysis buffer was added to allow for complexes to form. Anti — N2 and anti- N1 IgY antibodies were subsequently added to form either the (anti-N1 IgY)-(N protein)-(anti-N2 IgY) complex or (anti-N2 IgY)-(N protein)-(anti-N1 IgY) complex as sandwiched complexes. The plates were developed using HRP labeled anti-IgY and substrate. Between each of the additions, the plates were blocked and washed as is typically done in standard ELISA protocols. NC, CPC and PC are similar to those in Example No. 1.

N protein at 10ng was detectable and the sensitivity of the assay was slightly (<20%) diminished when the antigen (N protein) was applied with lysis buffer (Table 3). In conclusion, the lysis buffer could be included to disrupt the virus in the sample to be evaluated in the assay.

Table 3: Quantitative detection of full-length N-protein by Sandwich ELISA

Example 3: Development of LFA for the detection of N Protein using IgY antibodies In this example, anti-N2 IgY antibody is coated/bound to the membrane at the test window and anti-IgY is bound to the membrane at the control window. Gold conjugated anti-N1 IgY and non- specific IgY is placed in the conjugate pad (see figures 5 for schematic view of the LFA design). 150uL of 10 ng/mL (1.5 ng or 1500 pg of N protein) or 5 ng/mL (0.75 ng or 750 pg of N protein) are placed in the sample well of the LFA in lysis buffer where it complexes with gold conjugated anti-N1 antibody. The complex is allowed to migrate and the migrated complex is captured at the test window by anti-N2 IgY antibody and also captured at the control window by anti-IgY antibody. Table 4: Reagent specifications

A signal at the control window is indicative of successful migration of the complex as schematically shown in Figure 7 (A and B). The test is valid only when a band is observed at the control window. Observance of a band at the test window is indicative of successful detection of the complex as shown in Concept A in Figure 4.

In a design similar to the above using unlabeled IgY against N2 at the test window and using biotin- gold labeled anti-N2 IgY as depicted in concept B in Figure. 4 would also yield similar results. The result is that 150 μL N protein at 10 ng/mL and 5 ng/mL are detected at the test window by both complexing designs using 2 different IgY antibodies, one to each domain or through the use of the same anti-domain IgY antibodies (Table 4, Figure 7).

Example 4. Development of LFA for the detection of N Protein at Ing/mL

In this example, 2mg/mL of anti-N2 IgY antibody is coated/bound to the membrane at the test window and anti-IgY is bound to the membrane at the control window. Gold conjugated anti-N1 or anti-N2 IgY at 20ug/mL and non-specific IgY at 10ug/mL is placed in the conjugate pad. 150uL of 10 ng/mL (1.5 ng or 1500 pg of N protein) or 5 ng/mL (0.75 ng or 750 pg of N protein) or Ing/mL (0.15ng or 150 pg of N protein) are placed in the sample well of the LFA in lysis buffer as same as example 3, where it complexes with gold conjugated anti-N1 IgY or anti-N2 IgY antibody. The complex is allowed to migrate and the migrated complex is captured at the test window by anti-N2 IgY antibody and also captured at the control window by anti-IgY antibody.

This approach has increased the sensitivity levels unto Ing/mL of full-length N protein in lysis buffer, as pictured in Figure 7.

Example 5: Detection of N protein by polyclonal anti-N- IgY and monoclonal anti-N-IgG combination of antibodies

In this example, the anti-N2-IgY polyclonal antibodies were coated on membrane at 2.5mg/mL. The anti-N mouse monoclonal IgG antibodies were used as a detector antibodies at 10ug/mL conjugated with gold nanoparticles. To the test device 150uL of N-protein from different concentrations i.e lug/mL (150ng of N protein loaded) or 100ng/mL (15ngof N protein loaded) or 10ng/mL (1.5ng of N protein loaded) or 1 ng/mL (0.15 ng of N protein loaded) or 100pg/mL (15pg of N protein loaded) or 10pg/mL (1.5pg of N protein loaded). The results captured in Figure 8 indicate the level of detection (LOD) of full-length N protein up to 1 ng/mL.

Example 6

Evaluation of a Dot Blot/Fast Flow design using combination of anti-N2 IgY and anti-N1 IgY Dot blot is a simple, fast thru-put method to detect antigens and antibodies in biological samples. Dot blot assays can be converted to Fast Flow device kits in the market place by adapting it into a device. The applicants have designed a dot blot system to detect N protein in saliva samples and validated its detection using the two antibodies using the following protocol

1. Spotting 1 mg/ml of anti-N1 or N2-IgY onto the nitrocellulose membrane

2. Allowing it to dry for two hors

3. Washing the membrane 3 times with phosphate buffered saline (wash buffer)

4. Blocking the membrane with 3% fetal calf serum solution for 1 hour

5. Washing with wash buffer 3 times

6. Adding either N1 or N2 antigen at desired concentration in the presence or absence of human saliva followed by washing three times with wash buffer

7. Detection by adding either anti-N1 or N2 -IgY again (at 1 mg/ml) and incubation for 1 hr.

8. Washing 3 times with wash buffer

9. Adding HRP coupled anti-IgY for color development.

The results indicated that the dot blot for detection of either N1 or N2 antigens using respective N1 or N2 anti-IgY for capture and detection. Both antigens are clearly detectable at 10 μg/ml and 1 μg/ml (Figure 9). Figure 10 shows the same experiment using lower concentrations of N1 or N2 antigens and demonstrates detection even at 0.25 μg/ml of antigen. Figure 11 shows the detection of full-length N protein using an N2 capture and detection system as described above. The inventors have performed this experiment since N2/N2 anti-IgY combination produced stronger signal compared to N1/N1 anti-IgY combination. The first three strips show detection of undiluted N protein added to the dot blot and the next three blots are saliva spiked N protein, showing detection but reduced possibility due to the dilution with saliva.

This dot blot method demonstrated the detection of N protein up to 250 pg and can be adapted to a Fast Flow spot device.

Example 7 Clinical evaluation of kit with patient’s saliva samples

In this example, saliva is collected from the covid positive (confirmed by RT-PCR with Ct value of

22) patient (Table 5) and mixed equally with lysis buffer at 1:1 dilution in a microfuge tube. 150 μL of the mixed solution was then added on to the sample dropping point in the LFA kit and allowed to migrate for 3-5 minutes.

Table 5. RT-PCR report of the Covid positive sample

The two pink bands appeared in the test kit has clearly demonstrated the detection of covid positive sample in the LFA kit (Figure 12).

Claims

CLAIMS We Claim:

1. A process of producing antibodies comprising raising anti-domain 1 and anti-domain 2 antibodies against two different domains of a single antigen wherein anti-domain 1 antibody captures domain 1 and anti-domain 2 antibody detects domain 2 of the said antigen or anti- domain 1 antibody captures domain 2 and anti-domain 2 antibody detects domain 1 of the said antigen.

2. The process of producing antibodies as claimed in claim 1 wherein the said antigen is N antigen of SEQ ID NO. 1, domain 1 is SEQ ID NO. 2 and domain 2 is SEQ ID NO. 3.

3. The process of producing antibodies as claimed in claim 1 wherein the antibody raised against the said antigen is selected from IgY polyclonal antibodies, monoclonal antibodies, binding proteins isolated using phage display method, polyclonal IgGs and camelid nanobodies

4. The process of producing antibodies as claimed in claim 1 wherein the said antibodies are used in diagnostic assays selected from the group consisting of lateral flow, direct and indirect ELISA, dot blot and fast flow.

5. The process of producing antibodies as claimed in claim 1 wherein the said diagnostic assays use bodily fluids as sample selected from the group consisting of saliva, nasal secretions, sweat, serum, plasma and blood.

6. A method of use of antibodies raised against two domains of the same antigen as a theranostic and in imaging techniques.

7. The method of use of antibodies as claimed in claim 6 wherein the said antigen is N antigen of SEQ ID NO. 1, domain 1 is SEQ ID NO. 2 and domain 2 is SEQ ID NO. 3.