WO2022129947A1

WO2022129947A1 - Modified sars virus spike protein subunit

Info

Publication number: WO2022129947A1
Application number: PCT/GB2021/053366
Authority: WO
Inventors: Richard Tedder; Myra Mcclure; Petr Cherepanov
Original assignee: Imperial College Innovations Limited; The Francis Crick Institute Limited
Priority date: 2020-12-18
Filing date: 2021-12-17
Publication date: 2022-06-23
Also published as: GB202020199D0

Abstract

The present invention provides a modified SARS-CoV spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising: N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, H207 and/or L226; and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

Description

MODIFIED SARS VIRUS SPIKE PROTEIN SUBUNIT

Background

The present invention relates to a modified severe acute respiratory syndrome coronavirus (SARS-CoV) “spike protein” demonstrating reduced affinity for tetrapyrrole compounds, and to use thereof in methods for detecting antibody/ antibodies to SARS-CoV, particularly SARS-CoV-2, in a sample. Also provided are immunogenic compositions (e.g. vaccines) comprising such modified polypeptides.

SARS-CoV-2 is a strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory illness characterised by the COVID-19 pandemic. The World Health Organization declared the pandemic a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. As of 16 December 2020, almost 74 million cases were reported worldwide, resulting in almost 1 , 644, 889 deaths. Almost a year later (as of 10 December 2021), the number of reported cases had risen to over 268 million, resulting in more than 5.3 million reported deaths.

Key to ‘flattening’ the coronavirus curve is (just like many other transmissible infections) the availability of reliable, rapid tests to detect infected individuals, who can then isolate from others to prevent transmission. Indeed, countries (such as South Korea) in which vigilant testing and tracing strategies were adopted early on during the pandemic succeeded in suppressing COVID-19 cases to numbers much lower than those seen in other countries, with such success being largely attributed to the widespread availability of testing. Testing is all the more important where there is a lack of a vaccine, and is an important resource for mitigating anxiety about spreading SARS-CoV-2 even where symptoms of COVID-19 are not being exhibited. Although a number of vaccine options have subsequently become available, the need for vigilant testing has not waned.

As vaccine development progresses, it is hoped that widespread vaccination will play a key role in suppressing SARS-CoV-2 circulation.

Currently available tests include those for detecting the presence of the SARS-CoV-2 virus, and those for detecting the host response to the virus. These are molecular or antigen tests on the one hand (e.g. PCR-based or antigen tests) and antibody tests on the other hand (serological tests). Molecular tests (which detect viral genome) and antigen tests (which detect viral expression) can only diagnose the presence of infection as one finds in acute cases of COVID-19. They also do not inform the immune status of an individual who has received a vaccine. Whilst these methods can provide high levels of sensitivity, they are only of value for investigation and identification of the infected patient from whom body fluids may be drawn that contain virus genome. Given the potentially short duration of viral replication and expression of viral antigens, coupled with the presence of mild clinical symptoms in some patients, the question of past infection is often raised at a time that a diagnosis based on the detection of virus (e.g. viral DNA or antigen) is not possible. In addition, from a public health point of view of monitoring SARS-CoV-2 activity in a population of asymptomatic individuals, direct tests for virus will not inform the prevalence of past infection.

Turning now to suitable sampling and testing scenarios, whilst considerable time and effort have been invested with home-based strategies, inherent specificity and sensitivity limitations plus inevitable inaccuracies due to incorrect use of reagents have meant that this preferred diagnostic setting remains unrealised. In addition, a major criticism of such procedures and their home use is that they are not subject to any form of quality assurance. As such, home-based strategies are considered unsuitable (if not unacceptable) means for defining seroprevalence and in theory "immune status".

Advantageously, serological tests detecting anti-SARS-CoV-2 antibodies have the potential to detect both past and present infection, even cases of infection with mild or no symptoms. Understanding if a patient has been previously infected with SARS-CoV-2 and defining whether antibody levels remain stable in the recovering patient will be an important step in understanding the durability and importance of post-infection susceptibility to reinfection. Such a serological test could also show the extent of viral spread in a community and provide useful public-health information. Furthermore, serological tests will prove indispensable to aid our understanding of the effectiveness (over time) of vaccines, allowing for the antibody levels in a vaccine-receiving individual to be probed and assessed as a readout of the immunisation response and potentially protection.

Serological testing may also be appropriate to confirm immune responses in vaccinated individuals. Another approach to assess efficacy of vaccination is through determination of neutralization titres of serum; however, neutralisation assays may be less cost effective and may be not feasible on the population scale.

A large number of rapid diagnostic tests targeting antibodies to SARS-CoV-2 are commercially available. By way of example, relevant as of 5 September 2020, a total of 189 were listed by FIND foundation [https://www.finddx.org/]. However, the performance of those assays is neither consistent nor satisfactory, and is not amenable to quality assurance, see for example:

C. Atchison et al., Clin. Infect. Dis. Aug. 2020, doi: 10.1093/cid/ciaa1 178;

B. Flower, et al., Thorax, p. thoraxjni-2020-215732, Aug. 2020, doi: 10.1136/thoraxjni-2020-215732; and

M. Ricco, et al., J. Clin. Med. vol.9, no.5, p. 1515, May 2020. Doi: 10.3390/jcm9051515.

Whilst a few of these assays have received UK government approval:

- Abbott and Roche assays (for detecting IgG antibodies to the NP of SARS-CoV-2); and

Fortress/ Wantai assay (for detecting antibodies to the RBD of SARS-CoV-2) performance and reliability limitations issues remain.

For example, a recent study published by Public Health England (PHE) entitled “Evaluation of the Abbott SARS-CoV-2 IgG for the detection of anti-SARS CoV-2 antibodies” [https://assets.publishing.service.gov.uk/] found the Abbott test to have a specificity of 100% and overall sensitivity of 92.7%. However, a subsequent study (Rosadas C, Randell P, Khan M, McClure MO, Tedder RS. Testing for responses to the wrong SARS-CoV-2 antigen? Lancet. 2020 Sep 5;396(10252):e23. doi: 10.1016/S0140-6736(20)31830-4. Epub 2020 Aug 28. PMID: 32866429; PMCID: PMC7455229, incorporated herein by reference) graphically displayed the serious loss of sensitivity of the Abbott anti-NP assay. Whilst the apparent sensitivity of the government approved assays may be adequate, a failure to detect antibody, particularly during the acute infection and when applied to population-based seroprevalence surveys, may allow current and past infections to go un-recognised. This will naturally underascertain the prevalence of this infection in any community. More importantly, false-reactivity has the potential to lead an individual to believe that having had the infection (which may have passed) and that they may be protected to some extent against reinfection. Though it cannot be guaranteed that the recovery confers resistance to reinfection, the double risk of falsely believing that one has had the infection when (when one has in fact not had the infection) is clearly dangerous.

Both the Abbott and the Roche formats require direct input of plasma/ serum and are, as a result, variously sensitive to and perturbed by the presence of an analyte, which may vary considerably in the level of included serum/ plasma. Furthermore, neither of these assays provides any direct data on the presence of antibody that is likely to be able to neutralise viral infectivity.

As the demand for antibody-testing increases, so too will the need for greater assurances over assay performance and robustness. In particular, there is a need for improved reagents for increasing the reliability and accuracy of test kits.

Summary of the Invention

The present invention solves one or more of the above-identified problems by providing an improved “antigen reagent” for use in serology tests, in which a virus “spike protein” (S1) sequence has been modified thus significantly improving the performance of existing tests that otherwise use the “wild-type” S1 sequence. In summary, the modified S1 is better equipped to bind antibodies than a corresponding wild-type sequence. Thus, not only have the inventors identified a route to improvement of existing kits, but have provided the solution via modified S1.

Noting that S1 contains key epitopes (e.g. within the RBD) for antibody detection of SARS- CoV viruses (including SARS-CoV-2), this modified S1 also finds utility in patient vaccination.

In more detail, the present invention is predicated on the surprising finding that the SARS- CoV (more particularly SARS-CoV-2) spike protein (a glycoprotein that is the dominant viral antigen and the target of neutralising antibodies) binds biliverdin and bilirubin, tetrapyrrole products of haem metabolism, with nanomolar affinity. As explained in the Examples, the inventors have identified a tetrapyrrole interaction pocket within a deep cleft on the spike N- terminal domain (NTD) and have found the presence of biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of NTD-specific neutralising antibodies. The inventors’ work indicates that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope.

This is important, as the spike protein, most particularly the S1 subunit (in which the tetrapyrrole interaction pocket has been identified) is regularly used as an antigen component in serology tests, as well as a key immunogenic antigen in vaccine compositions. With regard to the former, tetrapyrrole compounds (e.g. biliverdin) can be found in the blood, such that using blood/ plasma samples in serology tests will actually introduce tetrapyrrole compound(s) to the system, dampening interaction between S1 antigen (test reagent) and antibodies in the sample to be detected (thus inhibiting detection). Tetrapyrrole compounds (e.g. biliverdin) are also produced by cells in tissue culture conditions, such that recombinantly manufactured S1 may (at least partially) have ‘masked’ epitopes due to tetrapyrrole binding.

As outlined in detail in the Examples (particularly at Example 2), the tetrapyrrole binding pocket has been mapped to the following amino acid residues of S1 (SEQ ID NO: 1): N99, 1101 , W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, H207 and L226. Closer interactions between biliverdin and S1 are seen with SARS CoV-2 S1 amino acid residues N99, W104, 1119, N121 , V126, F175, M177, R190, F192, H207, and L226.

The strongest interactions were seen with SARS-CoV-2 S1 residues N121, R190 and H207. Taking these residues thus as exemplary modification sites to disrupt the binding pocket, modified S1 ‘mutant’ polypeptides were generated, having highly conservative substitutions at these positions (N121Q, R190K and H207A). The mutant S1 polypeptides demonstrated significantly reduced affinity for biliverdin. Noting that even conservative substitutions suppress the interaction between biliverdin and S1 (and lead to improved performance in serology tests as will be described below) the skilled person would appreciate that any other (e.g. less conservative) amino acid change also provides for suppressed biliverdin binding.

Furthermore, because tetrapyrrole binding pocket contains a histidine residue (H207), the Applicant rationalised that the interaction may be pH-dependent. They found that treating the S1 -biliverdin complex with acids allowed purification of biliverdin-depleted spike antigens (see Fig 2d). However, because biological samples (e.g. human serum or plasma) contain variable amounts of biliverdin and bilirubin, the spike mutant may be preferable for the use in serological assays.

Unexpectedly, replacing the ‘wild-type’ S1 of existing immunoassays (e.g. serological tests) with such mutant S1 significantly improved the performance of these tests, particularly in terms of improving reactivity between the antigen (S1) and antibodies in human sera (see Examples 5-6). These improved preparations of the spike protein antigen allow more sensitive detection of the antibodies. This is particularly important when antibody levels are low, for example, soon after exposure to the virus or vaccination.

It is remarkable that a small molecule with a footprint of 370 A², corresponding to only -0.9% of solvent-exposed surface (per spike monomer), competes with a considerable fraction of spike-specific serum antibody population. It is thus equally remarkable that suppressing the S1-tetrapyrole interaction in immunoassays improves the performance of such assays.

The invention thus provides a modified S1 demonstrating lower affinity for a tetrapyrrole compound (e.g. lower epitope masking due to tetrapyrrole binding) compared to an unmodified equivalent.

Detailed Description

The term “modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide” may be referred to throughout as “modified S1”.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, H207 and/or L226 (more particularly N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, and/or H207; even more particularly N99, N121 , F175, M177, F194, and/or I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

For example, said at least one amino acid change may be at a location on the modified S1 polypeptide sequence that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, and/or H207.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and L226 (more particularly N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, and H207; even more particularly N99, N121 , F175, M177, F194, and I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to a polypeptide location, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and/or L226 (more particularly N99, 1101 , W104, 1119, N 121 , V126, F175, M177, R190, F192, F194, I203, and/or H207; even more particularly N99, N121 , F175, M177, F194, and/or I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to a polypeptide location, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and L226 (more particularly N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, and H207; even more particularly N99, N121 , F175, M177, F194, and I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a position on the modified S1 polypeptide sequence that corresponds to an amino acid position, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and/or L226 (more particularly N99, 1101 , W104, 1119, N 121 , V126, F175, M177, R190, F192, F194, I203, and/or H207; even more particularly N99, N121 , F175, M177, F194, and/or I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

In one aspect, the invention provides a modified SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a position on the modified S1 polypeptide sequence that corresponds to an amino acid position, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101, W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and L226 (more particularly N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, and H207; even more particularly N99, N121 , F175, M177, F194, and I203); and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

As the presence of a methionine residue at position 1 of a sequence having such methionine (e.g. as a start codon), such as SEQ ID NO: 1, is optional, the skilled person will take the presence/absence of the methionine residue into account when determining amino acid residue numbering. For example, where SEQ ID NO: 1 includes a methionine, the position numbering will be as defined above (e.g. N99 will be N99 of SEQ ID NO: 1). Alternatively, where the methionine is absent from SEQ ID NO: 1 the amino acid residue numbering should be modified by -1 (e.g. N99 will be N98 of SEQ ID NO: 1). Similar considerations apply when the methionine at position 1 of the other polypeptide sequences described herein is present/absent, and the skilled person will readily determine the correct amino acid residue numbering using techniques routine in the art.

In one aspect, the invention provides a method for producing a SARS coronavirus (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide that demonstrates lower binding affinity for said tetrapyrrole compound compared with S1 that is not prepared by the method, the method comprising: contacting an S1 polypeptide with a buffer having a pH of less than or equal to pH 6.0 (preferably less than pH 6.0) wherein said contacting step reduces the binding affinity of the S1 for said tetrapyrrole compound compared with S1 that is not contacted with said buffer.

Also provided is an S1 polypeptide obtainable by said method. The S1 may comprise or consist of a wild-type S1 sequence (e.g. SEQ ID NO. 1), or a fragment thereof. Such fragment may comprise or consist of amino acid residues 15-530.

The buffer may have a pH of 3-6, preferably 4.5-5.5. For example, a pH of about 5.2 is particularly suitable.

A preferred buffer is sodium acetate buffer (e.g. at pH 5.2). The amino acid change occurs within a “tetrapyrrole binding pocket” (of the modified S1 polypeptide) relative to the wild-type S1 sequence (SEQ ID NO: 1). By “binding pocket”, it is meant herein a region of the S1 sequence which comprises one or more amino acids which are the contact points (e.g. via hydrogen-bond, van der Waals interactions, and/or 71-71 stacking between amino acid side chain and ligand) for binding to the corresponding binding site of a tetrapyrrole compound, and/or which provide the space to accommodate other substrate amino acid residue(s) (e.g. by modification, such as by substitution) capable to bind a tetrapyrrole compound. The term “binding to” as used herein means “suitable for binding to” and forms part of Applicant’s rationale for the present invention - said rationale does not constitute an essential technical feature of the present invention. For example, the binding pocket, which may be defined by N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and L226 of SEQ ID NO: 1 , refers to a region of the S1 comprising amino acids N99, 1101 , W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, H207 and L226, and/or mutants thereof as described herein that Applicant believes cooperate to bind to a predicted binding site on a tetrapyrrole compound (particularly biliverdin).

The term “binding site” refers herein to a region of a tetrapyrrole compound comprising one or more groups that can be bound by the corresponding S1 binding pocket. For example, Pyrroles A and B of biliverdin represent a binding site, and are involved in a 71-71 stacking with an amino acid of the S1 binding pocket (e.g. a side chain of Arg190). The term “binding site” as used herein simply means “predicted binding site” (as predicted by Applicant) and forms part of Applicant’s rationale for the present invention - said rationale does not constitute an essential technical feature of the present invention.

Without wishing to be bound by any theory, it is believed that the above-defined S1 tetrapyrrole binding pocket effects an S1 -ligand association within a deep cleft on the spike N-terminal domain (NTD) e.g. the pocket providing a stabilising interaction between S1 and the ligand. Surprisingly, even modest (e.g. conservative) substitutions at individual amino acid residues within the binding pocket may significantly reduce the S1 affinity for the ligand.

Thus, the present invention is predicated on the surprising finding (e.g. unexpected technical effect) that targeted amino acid substitutions as claimed allow for the generation of S1 constructs that remain free (e.g. substantially free) of bound tetrapyrrole compound, such as biliverdin. The present inventors have not only successfully identified suitable amino acid positions of S1 which can be altered (e.g. substituted) to decrease tetrapyrrole binding, but have also identified precise amino acid changes which provide this effect.

A key advantage of reducing/ preventing binding to tetrapyrrole binding is that the unbound S1 demonstrates improved epitope presentation, e.g. allowing for stronger binding of anti- SARS-CoV-2 antibodies (and thus improved detection thereof in immunoassays as will be described in more detail below). Again, not wishing to be bound by any theory, it is believed that S1 undergoes conformational rearrangements in the absence of tetrapyrrole (e.g. biliverdin) binding, allowing antibodies to bind to S1 epitope(s). It is believed that access to the epitope is gated by a solvent-exposed loop composed of predominantly hydrophilic residues (“gate”, e.g. SARS-CoV-2 spike residues 174-188). To allow antibody binding, it is believed that the loop swings out of the way, with a backbone displacement in the middle of the loop of ~15 A (see Fig. 1b). The gating mechanism is believed to be controlled by insertion of Phe175 and Met177, which are located in the beginning of the loop, into the hydrophobic pocket vacated by biliverdin (Fig. 1b).

As described in the Examples, it has been identified that the pocket is lined by hydrophobic residues (He101, Trp104, Ile119, Val126, Met177, Phe192, Phe194, He203, and Leu226), which the inventors believe form van der Waals interactions with the tetrapyrrole ligand (e.g. biliverdin). As such, it is believed that effecting an amino acid change at any one of said positions disrupts van der Waals interactions between S1 and the tetrapyrrole ligand (e.g. biliverdin).

Biliverdin packs against His207, which projects its Ns2 atom towards pyrrolic amines, approaching three of them at ~3.6 A (see Example 2). As such, it is believed that effecting an amino acid change at His207 disrupts projection of an S1 amino acid Ns2 atom toward the tetrapyrrole ligand (e.g. biliverdin).

Pyrroles A and B (e.g. of biliverdin) are involved in a 71-71 stacking with side chain of Arg190. As such, it is believed that effecting an amino acid change at Arg190 disrupts a 71-71 stacking interaction of an S1 amino acid with the tetrapyrrole ligand (e.g. biliverdin). Said 71-71 stacking (with side chain of Arg190) is stabilised by hydrogen bonding with Asn99 (see Example 2). As such, it is believed that effecting an amino acid change at Asn99 disrupts stabilisation of said 71-71 stacking (with side chain of Arg190). Ligand (e.g. biliverdin) binding largely buries the side chain of Asn121, which makes a hydrogen bond with the lactam group of pyrrole D (see Example 2). As such, it is believed that effecting an amino acid change at Asn121 disrupts such hydrogen bond between an S1 amino acid and the tetrapyrrole ligand (e.g. biliverdin).

A modified S1 described herein may demonstrate a binding affinity for said tetrapyrrole compound that is 2-5 times lower (preferably 2-3 times lower) compared with wild-type S1 - see the data described in Example 3.

When comparing a modified S1 of the invention with a wild-type S1 , it will be appreciated that the polypeptide sequences of the modified S1 and the wild-type S1, other than the amino acid change, will otherwise be preferably identical. For example, if the modified S1 comprises or consists of amino acid residues 15-530 of S1 (in which the amino acid change is present), the wild-type S1 will likely preferably also comprise or consist of amino acid residues 15-530 of S1 (in which the amino acid change is not present).

A “SARS coronavirus” (or SARS-CoV) is a virus that causes Severe acute respiratory syndrome (SARS), a viral respiratory disease. Examples include MERS-CoV (e.g. a beta coronavirus that causes Middle East Respiratory Syndrome, or MERS), SARS-CoV (e.g. a beta coronavirus that causes severe acute respiratory syndrome, or SARS) and SARS-CoV- 2 (e.g. a coronavirus that causes coronavirus disease 2019, or COVID-19). Such coronaviruses each have highly homologous spike protein (including S1 subunit) sequences.

In all aspects and embodiments described throughout this specification, the SARS coronavirus is preferably SARS-CoV-2.

Reference to “SARS-CoV-2” means the strain of coronavirus that causes COVID-19 (e.g. having the sequence of NCBI reference no: NC_045512), and may be used interchangeably with the terms “2019 novel coronavirus” (2019-nCoV), and “human coronavirus 2019” (HCoV-19 or hCoV-19).

“Tetrapyrrole compounds” are a class of chemical compounds that contain four pyrrole or pyrrole-like rings. The pyrrole/pyrrole derivatives are linked by (=(CH)- or -CH2- units), in either a linear or a cyclic fashion. Pyrroles are a five-atom ring with four carbon atoms and one nitrogen atom. Tetrapyrroles are common cofactors in biochemistry and their biosynthesis and degradation feature prominently in the chemistry of life. Exemplary tetrapyrrole compounds include haem breakdown products, such as bilirubin and biliverdin. A preferable tetrapyrrole compound is biliverdin:

(biliverdin).

The modified S1 as described herein may comprise an amino acid sequence having at least 60%, for example, at least 70% or at least 80% or at least 85% or at least 90% or at least 95% or at least 97% or at least 98% or at least 99%, sequence identity to the wild-type S1 (SEQ ID NO: 1), e.g. with the proviso that said modified S1 comprises said amino acid change within a tetrapyrrole binding pocket. The modified S1 amino acid sequence has less than 100% sequence identity to a wild-type S1 (e.g. SEQ ID NO: 1), e.g. because of said at least one amino acid change. Reference throughout this specification to a modified S1 embraces functional fragments thereof, that is fragments of said S1 that bind to anti-SARS- CoV (e.g. anti-SARS-CoV-2) antibodies at an equivalent or greater level than wild-type S1. For example, a modified S1 of the invention preferably comprises at least 400 (for example, at least 450 or at least 500) amino acids. By way of example, the N-terminal fourteen amino acids (e.g. cleavable signal peptide) and/ or the carboxyl-terminus (for example, amino acids 531-685) of S1 are not required for antibody binding, and indeed constructs corresponding the amino acid residues 15-530 of S1 have successfully been employed in serology tests for detecting anti-SARS-CoV-2 antibodies (see the Examples), such constructs (amino acid residues 15-530 of S1) being embraced by the “modified S1” as claimed.

“Sequence identity” between amino acid or nucleic acid sequences can be determined by comparing a position in each of the sequences which may be aligned for the purposes of comparison. When a position in the compared sequences is occupied by the same nucleotide or amino acid, then the sequences are identical at that position. A degree of identity between amino acid sequences is a function of the number of identical amino acid sequences that are shared between these sequences. A degree of sequence identity between nucleic acids is a function of the number of identical nucleotides at positions shared by these sequences. To determine the “percentage of sequence identity” between two amino acid sequences or two nucleic acid sequences, the sequences are aligned for optimal comparison. For example, gaps can be introduced in the sequence of a first amino acid sequence or a first nucleic acid sequence for optimal alignment with the second amino acid sequence or second nucleic acid sequence. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, the molecules are identical at that position.

The percentage (%) of identity between the two sequences is a function of the number of identical positions shared by the sequences. Hence, the percentage of identity can be calculated by multiplying the number of identical positions by 100 and dividing by the length of the aligned region (overlapping positions), including gaps (only internal gaps, not the gaps at the sequence ends).

In this comparison, the sequences can be of the same length, or may be of different lengths. Identity scoring only counts perfect matches, and does not consider the degree of similarity of amino acids to one another.

Optimal alignment of sequences may be herein preferably conducted by a global homology alignment algorithm should the alignment be performed using sequences of the same or similar length, such as by the algorithm described by Needleman and Wunsch (Journal of Molecular Biology; 1970, 48 (3): 443-53), by computerized implementations of this algorithm (e.g., using the DNASTAR® Lasergene software), or by visual inspection. Alternatively, should the alignment be performed using sequences of distinct length (e.g. the amino acid sequence of the light-chain according to the invention versus the entire amino acid sequence of a naturally-occuring botulinum neurotoxin), the optimal alignment of sequences can be herein preferably conducted by a local homology alignment algorithm, such as by the algorithm described by Smith and Waterson (Journal of Molecular Biology; 1981, 147: 195- 197), by computerized implementations of this algorithm (e.g., using the DNASTAR® Lasergene software), or by visual inspection. The best alignment (i.e. , resulting in the highest percentage of identity between the compared sequences) generated by the various methods is selected. Examples of global and local homology alignment algorithms are well-known to the skilled practitioner, and include, without limitation, ClustaIV (global alignment), ClustalW (local alignment) and BLAST (local alignment). The skilled practitioner would further readily understand that the present invention embraces modified S1 polypeptides that are substantially homologous, and which retain the capacity to bind anti-SARS-CoV (e.g. anti-SARS-CoV-2) antibodies, i.e. functional variants or homologs. These functional variants or homologs can be characterized as having one or more amino acid mutations (such as an amino acid deletion, addition, and/or substitution) other than the ones disclosed herein with regard to the tetrapyrrole binding pocket, and which do not significantly affect the folding or epitope activity, in particular with regard to recognition by an anti-SARS-CoV (e.g. anti-SARS-CoV-2) antibody. For example, such mutations include, without limitation, conservative substitutions, small deletions (typically of 1 to about 30 amino acids), small amino- or carboxyl-terminal extensions (such as an amino-terminal methionine residue), addition of a small linker peptide of up to about 20-25 residues or of an affinity tag.

The modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to the whole amino acid sequence of wild-type S1 (e.g. amino acid residues 1-685 of S1 (SEQ ID NO: 1)), in which the at least one amino acid change is present. The skilled person would understand that the S1 polypeptide comprises an N-terminal cleavable signal peptide, e.g. which may be the first 13 to 15 amino acids of S1. Thus, any reference to a “spike protein S1 subunit (S1) polypeptide” or a “labelled antigen” (e.g. comprising a sequence of the S1 polypeptide) that comprises the N-terminal signal peptide is intended to encompass said polypeptide in the absence of said signal peptide.

The N-terminal 13-15 amino acid residues (signal peptide) are typically cleaved after expression. Thus, the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to amino acid residues 13-685 (preferably 15-685) of S1 (SEQ ID NO: 1), in which the at least one amino acid change is present.

The modified S1 sequence may cease after the receptor binding domain, RBD, sequence (which is at amino acid residues 319-541 of S1 (SEQ ID NO: 1)).

In one embodiment, the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to amino acid residues 1-541 of S1 (SEQ ID NO: 1), in which the at least one amino acid change is present. The N-terminal 13-15 amino acid residues (signal peptide) are typically cleaved after expression. Thus, the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to amino acid residues 13-541 (preferably 15-541) of S1 (SEQ ID NO: 1), in which the at least one amino acid change is present.

The inventors have found that the S1 sequence can be truncated even further, having improved purification properties while retaining immunogenic activity/ epitopes (indeed, such truncated version was used in the immunoassays in the Examples).

In one embodiment, the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to amino acid residues 1-530 of S1 (SEQ ID NO: 1), in which the at least one amino acid change is present. The N-terminal 13-15 amino acid residues (signal peptide) are typically cleaved after expression, and are thus optional. Thus, the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide may comprise or consist of a sequence (otherwise) corresponding to amino acid residues 13-530 (preferably 15-530) of S1 (SEQ ID NO: 1), in which the at least one amino acid change is present.

In one embodiment, the at least one amino acid change is at a location that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising N99, W104, 1119, N121, V126, F175, M177, R190, F192, H207 and/or L226.

The at least one amino acid change may be at a position that corresponds to an amino acid residue selected from N99, W104, 1119, N121, V126, F175, M177, R190, F192, H207 and L226, of wild-type S1 (SEQ ID NO: 1). For example, the at least one amino acid change may be at a position that corresponds to an amino acid residue selected from N99, W104, 1119, N121 , V126, F175, M177, R190, F192, and H207, of wild-type S1 (SEQ ID NO: 1).

In a preferable embodiment, the at least one amino acid change is at a location that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising N121, R190, and/or H207.

Preferably, the amino acid change may preferably be at a position that corresponds to an amino acid residue selected from N121, R190, and H207, of wild-type S1 (SEQ ID NO: 1). A modified S1 polypeptide of the present invention having a binding pocket mutation (for binding a tetrapyrrole) may comprise one or more amino acid residue changes relative to the wild-type S1 sequence, as herein before defined. By way of illustration, a modified S1 of the present invention may have a single amino acid residue mutation (within the binding pocket, as defined above), for example a mutation at a position corresponding to amino acid residue N121 of wild-type S1 (SEQ ID NO: 1). Similarly, a modified S1 polypeptide of the present invention may comprise more than one amino acid residue mutation (within the binding pocket as defined above), for example mutations at positions corresponding to amino acid residues N121 , R190K and H207 of wild-type S1 (SEQ ID NO: 1).

Thus, the modified S1 may comprise an amino acid change at 2 or more, 3 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more, or all 14 position(s) on the modified S1 polypeptide sequence that corresponds to an amino acid residue, of wild-type S1 (SEQ ID NO: 1), selected from: N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, H207 and L226. The modified S1 may comprise an amino acid change at 1 or more, 2 or more, 3 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, or all 11 position(s) on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, W104, 1119, N121, V126, F175, M177, R190, F192, H207 and L226, of wild-type S1 (SEQ ID NO: 1). The modified S1 may comprise an amino acid change at 1 or more, 2 or more, or all 3 position(s) on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N121, R190, and H207, of wild-type S1 (SEQ ID NO: 1).

For example, the modified S1 may comprise an amino acid change at positions on the modified S1 polypeptide sequence that corresponds to amino acid residues N121 , R190, and H207, of wild-type S1 (SEQ ID NO: 1).

The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of wild-type S1 (SEQ ID NO: 1); and optionally the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, 1101, W104, 1119, V126, F175, M177, R190, F192, F194, I203, H207 and L226 of wild-type S1 (SEQ ID NO: 1). The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, W104, 1119, V126, F175, M177, R190, F192, H207 and L226 of wild-type S1 (SEQ ID NO: 1). Preferably, the modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from R190 and H207 of wild-type S1 (SEQ ID NO: 1).

The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of wild-type S1 (SEQ ID NO: 1); and optionally the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, 1101, W104, 1119, N121, V126, F175, M177, F192, F194, I203, H207 and L226 of wild-type S1 (SEQ ID NO: 1). The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, W104, 1119, N121, V126, F175, M177, F192, H207 and L226 of wild-type S1 (SEQ ID NO: 1). Preferably, the modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N121 and H207 of wild-type S1 (SEQ ID NO: 1).

The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of wild-type S1 (SEQ ID NO: 1); and optionally the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, 1101, W104, 1119, N121 , V126, F175, M177, R190, F192, F194, I203, and L226 of wild-type S1 (SEQ ID NO: 1). The modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N99, W104, 1119, N121, V126, F175, M177, R190, F192, and L226 of wild-type S1 (SEQ ID NO: 1). Preferably, the modified S1 may comprise an amino acid change at a position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of wild-type S1 (SEQ ID NO: 1); and the modified S1 may comprise at least one further amino acid change at a position on the modified S1 polypeptide sequence that corresponds to an amino acid residue selected from N121 and R190 of wild-type S1 (SEQ ID NO: 1).

The terms “modification”, “change” or “mutation” can be used herein interchangeably, and refer to the alteration in the amino acid sequence compared to that of a protein of reference, i.e. herein relative to the wild-type S1 (SEQ ID NO: 1). The amino acid sequence illustrated herein as SEQ ID NO: 1 is 685 amino acid residues in length and ends with R685. It is understood that S686 is the first amino acid residue of the S2 subunit and most likely represents the C-terminal end of the S1 subunit. Thus, SEQ ID NO: 1 represents the subunit of the spike protein referred to as S1. In this regard, a wild-type S1 is typically 685 amino acid residues in length, which includes a short N-terminal signal peptide of about 13-15 amino acid residues.

As further explained below, the present invention reveals the identification of critical amino acid positions within a wild-type S1 that allow rational change to a different amino acid residue (or deletion of the amino acid) in order to render an S1 polypeptide incapable of (or having reduced capacity to) being bound by tetrapyrrole. In this regard, introduction of an amino acid change (i.e. a mutation), may be effected by means of an amino acid insertion, a deletion or a substitution, and preferably by means of an amino acid substitution. Methods allowing introduction of such mutation are known to the skilled person in the art. For example, it is possible to introduce a mutation by random or directed mutagenesis, by PCR using degenerate primers, e.g. in the nucleotide sequence coding for the protein of reference. Said techniques are notably described by Sambrook et al. in “Molecular Cloning: A laboratory Manual”, 4th edition, Cold Spring Harbor Laboratory Press, (2012, and updates from 2014), and by Ausubel et al. in “Current Protocols in Molecular Biology”, John Wiley & Sons (2012).

The amino acid change may be a deletion (e.g. designated by “del”). In such embodiments, the term “del” may be presented after recitation of the amino acid and its position e.g. as per the following: N99del, l101del, W104del, I119del, N121del, V126del, F175del, M177del, R190del, F192del, F194del, l203del, H207del, L226del. Other amino acid changes may include insertions, indels, duplications and frame shifts that lead to a lower level of tetrapyrrole binding compared to that for the wild-type S1. In a preferable embodiment, the amino acid change is a substitution.

The amino acid change may comprise substitution of N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, or L226 (positions corresponding to that of wild-type S1 , SEQ ID NO: 1) for any non-N, non-l, non-W, non-l, non-N, non-V1, non-F, non-M, non-R, non-F, non-F, non-l, or non-L amino acid, respectively. The amino acid change may comprise substitution of N99, W104, 1119, N121 , V126, F175, M177, F192, H207 or L226 (positions corresponding to that of wild-type S1, SEQ ID NO: 1) for any non-N, non-W, non-l, non-N, non-V, non-F, non-M, non-F, non-H or non-L amino acid, respectively. The amino acid change may comprise substitution of N121, R190, or H207 (positions corresponding to that of wild-type S1, SEQ ID NO: 1) for any non-N, non-R, or non-H amino acid, respectively.

Preferably, the amino acid change is a conservative substitution. For example, the amino acid change is preferably of a minor nature, that is a conservative amino acid substitutions (see below) and other substitutions that do not significantly affect the folding or activity of the polypeptide.

Basic: arginine, lysine, histidine

Acidic: glutamic acid, aspartic acid

Polar: glutamine, asparagine

Hydrophobic: leucine, isoleucine, valine

Aromatic: phenylalanine, tryptophan, tyrosine

Small: glycine, alanine, serine, threonine, methionine

In addition to the 20 standard amino acids, non-standard amino acids (such as 4- hydroxyproline, 6-N-methyl lysine, 2-aminoisobutyric acid, isovaline and a-methyl serine) may be substituted for amino acid residues of the polypeptides, of the present invention. A limited number of non-conservative amino acids, amino acids that are not encoded by the genetic code, and unnatural amino acids may be substituted for clostridial polypeptide amino acid residues. The polypeptides of the present invention may also comprise non-naturally occurring amino acid residues.

Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4- methano-proline, cis-4-hydroxyproline, trans-4-hydroxy-proline, N-methylglycine, allothreonine, methyl-threonine, hydroxy-ethylcysteine, hydroxyethylhomo-cysteine, nitroglutamine, homoglutamine, pipecolic acid, tert-leucine, norvaline, 2-azaphenylalanine, 3- azaphenyl-alanine, 4-azaphenyl-alanine, and 4-fluorophenylalanine. Several methods are known in the art for incorporating non-naturally occurring amino acid residues into proteins.

The amino acid substitution may comprise the substitution of an amino acid comprising a certain physiochemical property (e.g. hydrophobicity) with an amino acid having a similar or alternative property. Examples of such substitutions are listed below:

Acidic amino acid substituted for a neutral, polar amino acid;

Polar amino acid substituted for a non-polar amino acid;

Non-polar amino acid substituted for a non-polar amino acid;

Non-polar amino acid substituted for a polar amino acid;

Polar amino acid substituted for a basic amino acid;

Non-polar amino acid substituted for an acidic amino acid;

Non-polar amino acid substituted for a polar amino acid.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N99 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate (preferably glutamine).

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1101 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue W104 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Phenylalanine, and Tyrosine.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1119 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate. Preferably, an amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1) may be amino acid residue glutamine (e.g. N121Q).

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue V126 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Alanine, and Leucine.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F175 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Tyrosine and Tryptophan.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue M177 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Serine, Cysteine, Selenocysteine, and Threonine (preferably Serine, Cysteine, or Threonine).

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of lysine and histidine. Preferably, an amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1) may be amino acid residue lysine (e.g. R190K).

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F192 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Tyrosine and Tryptophan.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F194 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Tyrosine and Tryptophan.

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue I203 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine. An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of alanine, lysine, arginine, glycine, valine, leucine and isoleucine. Preferably, an amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wildtype S1 (SEQ ID NO: 1) may be amino acid residue alanine (e.g. H207A).

An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue L226 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, Isoleucine. An amino acid change at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue L226 of the wild-type S1 (SEQ ID NO: 1) may be an amino acid residue selected from the group consisting of Glycine, Valine, Isoleucine.

In one embodiment, the at least one amino acid residue change comprises: i. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N99 of the wild-type S1 (SEQ ID NO: 1); ii. an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1101 of the wild-type S1 (SEQ ID NO: 1); iii. an amino acid residue selected from the group consisting of Phenylalanine, and Tyrosine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue W104 of the wild-type S1 (SEQ ID NO: 1); iv. an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1119 of the wild-type S1 (SEQ ID NO: 1); v. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); vi. an amino acid residue selected from the group consisting of Glycine, Alanine, and Leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue V126 of the wild-type S1 (SEQ ID NO: 1); vii. an amino acid residue selected from the group consisting of Tyrosine and Tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F175 of the wild-type S1 (SEQ ID NO: 1); viii. an amino acid residue selected from the group consisting of Serine, Cysteine, Selenocysteine, and Threonine, at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue M177 of the wild-type S1 (SEQ ID NO: 1); ix. an amino acid residue selected from the group consisting of a lysine and histidine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); and/or x. an amino acid residue selected from the group consisting of Tyrosine and Tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F192 of the wild-type S1 (SEQ ID NO: 1); xi. an amino acid residue selected from the group consisting of Tyrosine and Tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F194 of the wild-type S1 (SEQ ID NO: 1); xii. an amino acid residue selected from the group consisting of Glycine, Alanine, Valine, and Leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue I203 of the wild-type S1 (SEQ ID NO: 1); xiii. an amino acid residue selected from the group consisting of an alanine, lysine, arginine, glycine, valine, leucine and isoleucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1); and/or xiv. an amino acid residue selected from the group consisting of a Glycine, Alanine, Valine, Isoleucine (preferably selected from Glycine, Valine, Isoleucine) at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue L226 of the wild-type S1 (SEQ ID NO: 1).

In one embodiment, the at least one amino acid residue change comprises: i. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); ii. an amino acid residue selected from the group consisting of a lysine and histidine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); and/or iii. an amino acid residue selected from the group consisting of an alanine, lysine, arginine, glycine, valine, leucine and isoleucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1). In a preferable embodiment, the at least one amino acid residue change comprises: i. a glutamine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); ii. a lysine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); and/or iii. an alanine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1).

Examples of modified S1 polypeptides (e.g. having a binding pocket change) include a modified S1 polypeptide comprising at least one of the following substitution(s):

- N121Q, N121 D, N121E

- R190L, R190H

- H207A, H207K, H207R, H207G, H207V, H207L, H207I

In summary, most preferable examples of modified S1 polypeptides (e.g. having a binding pocket change) include a modified S1 polypeptide comprising the substitution:

N121Q;

R190K; and/or (preferably or) H207A.

A particularly preferred modified S1 polypeptide comprises the substitution N121Q.

A further aspect of the present invention provides a nucleic acid construct, comprising or consisting of a nucleic acid sequence that encodes a modified SARS-CoV (e.g. SARS-CoV- 2) spike protein S1 subunit (S1) polypeptide as herein described. A nucleic acid construct of the invention may include conventional regulatory elements such as a promoter and/or a terminator. The term “nucleic acid” may be used synonymously with the term “polynucleotide”.

A nucleic acid construct described herein is preferably an isolated nucleic acid construct. The nucleic acid construct may be recombinant, synthetic, and/or purified.

In one embodiment, the nucleic acid construct is provided in the form of a bacterial plasmid or viral vector. Said nucleic acid construct can optionally be codon-biased for optimizing expression (e.g. recombinant expression) in a desired host cell (e.g. E.coli). In one embodiment, a nucleic acid construct encoding a modified SARS-CoV (e.g. SARS- CoV-2) spike protein S1 subunit (S1) polypeptide as herein described can be employed for administration to a patient, such as for therapeutic use. To this end, said nucleic acid construct can be typically optimised by way of conventional methodology for delivery into (followed by expression within) a target cell, preferably a human cell.

The nucleic acid construct may comprise DNA or RNA (preferably mRNA). An RNA nucleic acid construct may be particularly suited to nucleic acid immunisation.

The invention also provides a composition comprising (i) one or more nucleic acid(s) of the invention, or one or more nucleic acid(s) complementary thereto. Optionally, said composition further comprises a pharmaceutically acceptable carrier or excipient. In one embodiment, said composition is for use in nucleic acid immunisation.

Another aspect of the invention provides a host cell comprising a nucleic acid construct described herein. Said host cell may be a mammalian cell, an insect cell, a yeast cell, a bacterial cell (e.g. E. coli), or a plant cell. In a preferable embodiment, the host cell is a bacterial cell (preferably E. coli).

Another aspect of the invention provides a pseudotyped SARS-CoV (e.g. SARS-CoV-2) virus, wherein the pseudotyped virus comprises a modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described herein. The pseudotyped SARS-CoV (e.g. SARS-CoV-2) virus may be provided in the form of a pseudotyped virus particle (e.g. a “pseudovirus”). Additionally or alternatively, the pseudotyped SARS-CoV (e.g. SARS-CoV-2) virus may be provided in the form of a viral vector. The modified SARS-CoV (e.g. SARS- CoV-2) spike protein S1 subunit (S1) preferably replaces the wild-type S1 in the pseudotyped SARS-CoV-2 virus. However, the invention embraces embodiments in which the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) is present in addition to the wild-type S1.

Vaccination

A further aspect of the invention provides an immunogenic composition comprising a modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described herein, or a nucleic acid construct as described herein, or a pseudotyped SARS- CoV (e.g. SARS-CoV-2) virus as described herein. The immunogenic composition of the invention is typically a vaccine, preferably a subunit vaccine.

In one embodiment, the immunogenic composition comprises a pharmaceutically acceptable carrier or excipient. For the preparation of immunogenic compositions of the invention, the active immunogenic ingredients may be mixed with carriers or excipients, which are pharmaceutically acceptable and compatible with the active ingredient. Suitable carriers and excipients include, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the immunogenic composition may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, and/or adjuvants which enhance the effectiveness of the immunogenic composition.

In one embodiment, the immunogenic composition comprises an adjuvant. A non-limiting example of an adjuvant with the scope of the invention is aluminium hydroxide. Other nonlimiting examples of adjuvants include but are not limited to: N-acetyl-muramyl-L- threonyl-D-isoglutamine (thr-MDP), N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MOP), N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(T- 2'dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (CGP 19835A, referred to as MTP-PE), and RIBI, which contains three components extracted from bacteria, monophosphoryl lipid A, trehalose dimycolate and cell wall skeleton (MPL + TDM+CWS) in a 2 % squalene/ Tween 80 emulsion.

The invention embraces methods of immunising a patient with any one of: a modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described herein, a nucleic acid construct as described herein, a pseudotyped SARS-CoV (e.g. SARS-CoV-2) virus as described herein, an immunogenic composition as described herein; or any one of the above for use in a method of immunising a patient.

Methods of treatment embrace preventing, treating or suppressing a SARS-CoV (e.g. SARS- CoV-2) infection.

In one embodiment, the immunogenic composition is for use in raising an immune response in a patient. In a preferred embodiment, the immune response is a protective immune response. A protective immune response confers immunological cellular memory upon the subject, with the effect that a secondary exposure to the same or a similar antigen is characterised by e.g.

(a) shorter lag phase than after initial exposure to the antigen; (b) production of antibody which continues for a longer period than after initial exposure to the antigen; (c) a change in the type and quality of antibody produced in comparison to initial exposure to the antigen; (d) a shift in class response, with IgG antibodies appearing in higher concentrations and with greater persistence than IgM, than after initial exposure to the antigen; (e) increased average affinity (binding constant) of the antibodies for the antigen compared with initial exposure to the antigen; and/or (f) characteristics known in the art to characterize a secondary immune response.

In one embodiment, the immunogenic composition of the invention is for use in preventing, treating or suppressing SARS-CoV (e.g. SARS-CoV-2) infection in a patient. In one embodiment, the invention provides use of the immunogenic composition of the invention in preventing, treating or suppressing SARS-CoV (e.g. SARS-CoV-2) infection in a patient. In one embodiment, the invention provides a method of preventing, treating or suppressing SARS-CoV (e.g. SARS-CoV-2) infection in a patient, said method comprising administering to the patient the immunogenic composition of the invention.

The patient is typically a mammal. In one embodiment, the mammal is a human. In one embodiment, the mammal is non-human. Typical non-human patients include ungulates (typically cow, sheep or goat). Use of the invention with domesticated livestock is advantageous because it provides decreased risk of secondary transmission of SARS-CoV (e.g. SARS-CoV-2) infection to humans.

Thus, the present invention provides an effective means for preventing, treating or suppressing SARS-CoV (e.g. SARS-CoV-2) infection (or a symptom thereof).

In one embodiment, immunogenic compositions of the invention are used prophylactically to prevent the onset of SARS-CoV (e.g. SARS-CoV-2) infection in a patient. In such embodiments, the patient is typically at increased risk of becoming infected with SARS-CoV (e.g. SARS-CoV-2), e.g. healthcare or laboratory workers. Due to the reduced side effects associated with the protein antigens of the invention, immunogenic compositions of the invention may be used for widespread vaccination strategies. Immunogenic compositions for use in prophylaxis are administered at a prophylactically effective amount, i.e. they contain protein antigen(s) in any amount that, when administered alone or in combination to a patient, triggers an immune response against SARS-CoV (e.g. SARS-CoV-2), and so inhibits or delays the onset or recurrence of at least one of the clinical symptoms of SARS-CoV (e.g. SARS-CoV-2) infection. In one embodiment, the prophylactically effective amount prevents the onset or reoccurrence of the SARS-CoV (e.g. SARS-CoV-2) infection. "Inhibiting" the onset means either lessening the likelihood of the infection's onset, or preventing the onset entirely.

In one embodiment, immunogenic compositions of the invention are used to treat or suppress SARS-CoV (e.g. SARS-CoV-2) infection in a patient. In such cases, the patient is infected with SARS-CoV (e.g. SARS-CoV-2), or has a symptom of SARS-CoV (e.g. SARS- CoV-2) infection (e.g. symptoms from high fevers (up to 40-41 °C), severe headache, general malaise, myalgia, chills and/or sweats, non-productive cough, nausea, and chest pain). In one embodiment, treating or suppressing SARS-CoV (e.g. SARS-CoV-2) infection comprises administering a composition of the invention to the patient within 5 days of infection with SARS-CoV (e.g. SARS-CoV-2). In one embodiment, the composition is administered to the patient within 2 days of infection, preferably within 1 day of infection with SARS-CoV (e.g. SARS-CoV-2), more preferably within 12 hours of infection with SARS-CoV (e.g. SARS-CoV-2), most preferably within 6 hours of infection with SARS-CoV (e.g. SARS- CoV-2). Said "infection with SARS-CoV (e.g. SARS-CoV-2)” includes exposure to a sample suspected of containing, or known to contain SARS-CoV (e.g. SARS-CoV-2).

Administration of immunogenic compositions of the invention is generally by conventional routes e.g. intravenous, intramuscular, subcutaneous, intraperitoneal, or mucosal routes. The administration may be by parenteral injection, for example, a subcutaneous or intramuscular injection. In one embodiment, administration is intravenous. In one embodiment, administration is intraperitoneal. In one embodiment, administration is intramuscular.

The immunogenic compositions are administered in a manner compatible with the dosage formulation, and in such amount as will be effective for treatment, prevention and/or suppression of SARS-CoV (e.g. SARS-CoV-2) infection. The quantity to be administered (which may be for example in the range of 5 micrograms to 250 micrograms of antigen per dose) depends on the subject to be treated, capacity of the patient's immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered may depend on the judgment of the practitioner and may be particular to each patient.

The immunogenic compositions of the invention may be given in a single dose schedule, or optionally in a multiple dose schedule. A multiple dose schedule is one in which a primary course of vaccination may be with 1-6 separate doses, followed by other doses given at subsequent time intervals required to maintain and or reinforce the immune response, for example, at 1-4 months for a second dose, and if needed, a subsequent dose(s) after several months. The dosage regimen will also, at least in part, be determined by the need of the individual and be dependent upon the judgment of the practitioner.

Serology

A most advantageous property of the modified S1 polypeptide described herein is that it may be used to replace an otherwise equivalent S1 antigen employed in existing serology tests, improving the performance thereof. For example, by doing so, epitopes of the modified S1 are not (or less) suppressed due to binding of tetrapyrroles that may be present in the test sample (typically a blood sample).

The present inventors recently developed a “double antigen bridging assay” (DABA), using a sequence from wild-type S1 as a “capture means”, that demonstrates excellent performance (i.e. flawless 100% specificity determined on 850 samples that pre-date the emergence of SARS-CoV (e.g. SARS-CoV-2), and 98.9% sensitivity on sera) with plasma and serum samples. This is described in PCT/GB2021/051837 (claiming priority to UK patent application GB2011047.4), incorporated herein by reference in its entirety.

In a further piece of work, the present inventors introduced a human IgG and/ or IgM capture means (i.e. a capture means non-specific to SARS-CoV (e.g. SARS-CoV-2) antigens), using a sequence from wild-type S1 as a labelled antigen. This is described in PCT/GB2021/052305 (claiming priority to UK patent application GB2014047.1), incorporated herein by reference in its entirety.

In a most surprising development, incorporating a modified S1 polypeptide of the present invention improves the performance of such serology tests significantly, and more particular promotes signal such that the risk of a false-negative test is reduced. With regard to the “DABA” (e.g. hybrid DABA) assay, it is believed that the antibodies to the N-terminal domain (NTD) of S1 are not detected. Instead, the NTD helps by “presenting” the RBD to antibodies. It is believed that, in the presence of biliverdin, the hydrophobic core of the NTD is hidden (by biliverdin itself and by loop structures of the S1). In the absence of biliverdin binding, it is believed the loops open up (like flower petals) exposing the hydrophobic residues inside. It is believed this allows the NTD of the modified S1 polypeptide of the invention to “stick” to a solid-phase support (e.g. plastic of plate) and present the RBD for recognition of anti-SARS-CoV (e.g. SARS-CoV-2) antibodies.

With regard to the IgG/ IgM capture assay (and any assay, which detects antibodies to the NTD), it is believed that, in the absence of biliverdin binding, the hydrophobic core of the NTD is open for recognition by the antibodies. This is shown, for example, by solving the structure of S1 bound with antibody Fab P008_056 (see the Examples).

Both effects are related, of course, they both depend on the exposure of the hydrophobic core of the protein (to solid-phase support or anti-SARS-CoV-2 antibodies).

In one aspect, the invention provides a method for detecting the presence or absence of SARS-CoV (e.g. SARS-CoV-2) antibodies in a sample, the method comprising: a. contacting the sample with a solid-phase support having a first antigen immobilised thereto, i. wherein the first antigen comprises a modified SARS-CoV (e.g. SARS- CoV-2) spike protein S1 subunit (S1) polypeptide as described herein; b. allowing SARS-CoV (e.g. SARS-CoV-2) antibodies present in the sample to bind to the modified S1 polypeptide, thereby forming a complex of modified S1 polypeptide and SARS-CoV (e.g. SARS-CoV-2) antibody; c. contacting said complex with a labelled second antigen, wherein said labelled second antigen comprises a SARS-CoV (e.g. SARS-CoV-2) spike protein polypeptide (preferably wherein said labelled second antigen comprises or consists of a SARS-CoV receptor binding domain polypeptide, more preferably wherein said labelled second antigen comprises or consists of a sequence of SEQ ID No.: 4) that binds SARS-CoV (e.g. SARS-CoV-2) antibody; d. allowing said labelled second antigen to bind to SARS-CoV (e.g. SARS-CoV-2) antibody present in the sample; e. removing labelled second antigen that is not bound to said complex; and f. detecting the presence of labelled second antigen bound to said complex; wherein the presence of labelled complex indicates the presence SARS-CoV (e.g. SARS-CoV-2) antibody in the sample, and wherein the absence of labelled complex indicates the absence of SARS-CoV (e.g. SARS-CoV-2) antibody in the sample.

Such method represents the “DABA” (e.g. hybrid DABA) format serological test.

The labelled second antigen is preferably amino acid residues 319-541 of the SARS-CoV-2 spike protein (SEQ ID NO.: 4) conjugated to a label.

Said labelled second antigen is preferably present in a fluid phase.

In a further aspect, there is provided a method for detecting the presence or absence of SARS-CoV (e.g. SARS-CoV-2) antibody in a sample, the method comprising: a. contacting the sample with a solid-phase support having anti-human IgG antibody and/ or anti-human IgM antibody immobilised thereon; b. allowing anti-SARS-CoV (e.g. SARS-CoV-2) antibody (e.g. antibodies) present in the sample to bind to the immobilised anti-human IgG antibody and/ or antihuman IgM antibody, thereby forming an immobilised complex comprising said anti-human antibody and anti-SARS-CoV (e.g. SARS-CoV-2) antibody; c. contacting said immobilised complex with a labelled antigen, i. wherein said labelled antigen comprises the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described herein, that binds anti-SARS-CoV (e.g. SARS-CoV-2) antibody; d. allowing said labelled antigen to bind to anti-SARS-CoV (e.g. SARS-CoV-2) antibody (e.g. antibodies) present in the immobilised complex; e. removing unbound labelled antigen; and f. detecting the presence of labelled antigen; wherein the presence of labelled antigen indicates the presence of anti-SARS-CoV (e.g. SARS-CoV-2) antibody, and wherein the absence of labelled antigen indicates the absence of anti-SARS-CoV (e.g. SARS-CoV-2) antibody.

Such method represents the “IgG/ IgM capture” format serological test.

In said methods, the modified S1 preferably comprises an S1 receptor binding domain (RBD) sequence. For example, the modified S1 may comprise a sequence corresponding to amino acid residues 319-541 of wild-type (WT) S1 (SEQ ID NO.: 1), and more preferably comprises a sequence corresponding to amino acid residues 319-530 of WT S1 (SEQ ID NO.: 1). Without wishing to be bound by theory, it is believed that the NTD of S1 may help ‘present’ and RBD for detection by antibodies.

Said labelled antigen is preferably present in a fluid phase.

Suitable, such methods may further comprise recording the output of said method on a data readable format.

In a related aspect, there is provided an immunoassay solid-phase support for detecting the presence or absence of antibody to SARS-CoV (e.g. SARS-CoV-2) in a sample, the solidphase support comprising a first antigen immobilised thereto, a. wherein the first antigen comprises the modified SARS-CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described herein.

This may be provided in the form of a kit together with one or more further components.

Another aspect provides a kit for detecting the presence or absence of antibody to SARS- CoV (e.g. SARS-CoV-2) in a sample, the kit comprising: a. an immunoassay solid-phase support as described above, and b. a labelled second antigen, wherein said labelled second antigen comprises a SARS-CoV (e.g. SARS-CoV-2) spike protein polypeptide (preferably wherein said labelled second antigen comprises or consists of a SARS-CoV receptor binding domain polypeptide, more preferably wherein said labelled second antigen comprises or consists of a sequence of SEQ ID No.: 4) that binds SARS-CoV-2 antibody; optionally wherein the labelled second antigen is amino acid residues 319-541 of the SARS-CoV-2 spike protein (SEQ ID NO.: 4) conjugated to a label; or a. a solid-phase support having anti-human IgG antibody and/ or anti-human IgM antibody immobilised thereon, wherein said anti-human IgG and IgM antibodies are able to capture and immobilise anti-SARS-CoV (e.g. SARS-CoV-2) antibody in the sample; and b. a labelled antigen, wherein said labelled antigen comprises the modified SARS- CoV (e.g. SARS-CoV-2) spike protein S1 subunit (S1) polypeptide as described above, that binds anti-SARS-CoV (e.g. SARS-CoV-2) antibody. The kit may preferably further comprise instructions for use for detecting the presence or absence of antibody to SARS-CoV (e.g. SARS-CoV-2) in a sample, preferably in a dried blood spot eluate sample.

Corresponding use of a solid-phase support, or a kit, as described above, for detecting for detecting antibody to SARS-CoV (e.g. SARS-CoV-2) in a sample is also provided.

The labelled antigen (e.g. as it is expressed) may be referred to as an S1 construct, and preferably takes amino acid residues 1-530 of the SARS-CoV (e.g. SARS-CoV-2) spike protein, in which the amino acid change is present (e.g. the expression construction may comprise said amino acid residues 1-530). An advantage of this particular S1 construct is its high level of expression.

The skilled person would understand that the S1 polypeptide comprises an N-terminal cleavable signal peptide, e.g. amino acids 1-14 of S1. Thus, any reference to a labelled antigen (e.g. comprising a sequence of the S1 polypeptide, such as that in the paragraph above) that comprises the N-terminal signal peptide is intended to encompass said polypeptide in the absence of said signal peptide. The labelled antigen as secreted (from a cell) may comprise or consist of amino acid residues 15-530 of the SARS-CoV (e.g. SARS- CoV-2) spike protein, in which the amino acid change is present e.g. due to cleavage of amino acid residues 1-14 (the signal peptide). The labelled antigen as secreted (from a cell) may comprise or consist of amino acid residues 13-530 of the SARS-CoV (e.g. SARS-CoV- 2) spike protein in which the amino acid change is present, e.g. due to cleavage of amino acid residues 1-12 (the signal peptide). The invention also embraces variants of said sequences having less than 100% sequence identity thereto e.g. having further amino acid change(s) in addition to an amino acid change of the present invention (e.g. albeit with the proviso that such variant retains immunological reactivity with an anti-SARS-CoV-2 antibody).

The labelled antigen may be a recombinant protein. In a preferable embodiment, the labelled antigen is a recombinant protein.

In DABA formats as described above, the use of hybrid double antigens (e.g. amino acid residues modified S1 polypeptide for a first antigen, and amino acid residues 319-541 of the SARS-CoV-2 spike protein for a (e.g. labelled) second antigen) allows purification of the two different antigens separately, optionally providing excipients in the solid-phase protein which differ from (e.g. potential) excipients in the fluid-phase protein (a feature which is not present in a normal/ non-hybrid double antigen assay with identical proteins). Thus, the first and second (e.g. recombinant) antigens may be derived from different sources. For example, the first antigen may be derived from a first expression and purification process, and the second antigen may be derived from a second (different) expression and purification process. In other words, the solid-phase and the second labelled antigen components differ in their sourcing and are of different origin, for example sharing only the epitope against which the test is designed to detect antibody.

In a preferable embodiment, the first and/or (preferably and) second antigen is a recombinant protein.

A step of “removing labelled second antigen that is not bound to said complex” may be referred to as a wash step (e.g. in which a wash buffer is used wash away free labelled antigen, thus ensuring visualisation of the label in subsequent steps allows visualisation of labelled antigen that is bound to captured/ immobilised SARS-CoV antibody). Methods of the invention may comprise one or more additional wash steps. In one embodiment, a step of contacting said complex with a labelled antigen (e.g. step c)) is preceded by a step of removing labelled antigen (and any other component present in the sample, such as free antibody) that is not bound to the anti-SARS-CoV antibody (e.g. that does not form a complex of first antigen and antibody).

The labelled antigen is labelled to allow visualisation of the detection of (immobilised) antibody. Any antigen label may in principle be employed. For example, the label may itself provide an observable/ detectable signal (e.g. visible dye), or it may require an activation partner (e.g. horseradish peroxidase (HRPO) plus substrate). Suitably, said label is conjugated directly to the antigen (e.g. by chemical conjugation or as a fusion protein).

Examples of suitable labels include detectable labels such as radiolabels or fluorescent or coloured molecules, enzymatic markers or chromogenic markers - e.g. dyes that provide a visible colour change upon binding of the detection antibody to an antigen. By way of example, the label may be fluorescein-isothiocyanate (FITC), R- phycoerythrin, Alexa 532, CY3 or digoxigenin. The label may be a reporter molecule, which is detected directly, such as by detecting its fluorescent signal, or by exposure of the label to photographic or X-ray film. Alternatively, the label is not directly detectable, but may be detected, for example, in a two-phase system. An example of indirect label detection is binding of an antibody to the label.

In a preferable embodiment, the labelled antigen is labelled with an HRPO. Suitably, said HRPO labelled antigen is detected by means of an activation partner, e.g. a substrate that, when oxidized by HRP using hydrogen peroxide as the oxidizing agent, yields a characteristic colour change. Said activation partner may be one or more substrate selected from 3,3’,5,5’-Tetramethylbenzidine (TMB), 3,3'-Diaminobenzidine (DAB), 2,2'-azino-bis(3- ethylbenzothiazoline-6-sulphonic acid) (ABTS), o-phenylenediamine dihydrochloride (OPD), 3-amino-9-ethylcarbazole (AEC), AmplexRed, Homovanillic acid or Luminol. Preferably, said activation partner is the substrate TMB.

Thus, the presence or absence of labelled antigen bound to said complex is detected via a signal emitted from a label. Preferably, the presence of labelled second antigen bound to said complex is confirmed when a (the) signal detected is greater than a signal detected in a control assay, wherein the control assay comprises contacting the solid-phase support with a control (e.g. seronegative) sample lacking SARS-CoV antibody (e.g. lacking SARS-CoV antibodies that bind to the first antigen). For example, the sequence may be at least 50% greater than that of the control, for example at least 60%, 70%, 80%, 90%, 100% (preferably at least 70% greater than that of the control).

The signal detected in the control assay may be determined either prior to carrying out a method of the invention or at the same time as carrying out a method of the invention (preferably at the same time).

The skilled person understands that where the methods of the invention comprise a comparison step between two assays (e.g. between a “test assay” and a “control assay”) that conditions (e.g. assay conditions during the method) should be kept consistent. For example, the amount of sample used should be the same, as should the time conditions, etc. Where a comparison is made between two samples herein, suitably the samples are equivalent. For example, the samples being compared may be the same sample types (e.g. blood such as a Dried Blood Spot) and subjected to the same processing steps. Preferably, the samples are obtained from the same species (e.g. human). Any solid-phase support may in principle be employed. For example, conventional multi-well plates and lateral flow devices. Preferably, the solid-phase support is a multi-well plate (such as a 96 well plate).

In one embodiment, the sample is from a subject, typically an animal, most preferably a human. The subject may also be a non-human animal, such as a non-human mammal (examples of which include cat, dog, horse, ruminant (e.g. goat and/or sheep), bovine animal (e.g. cow)). The terms “subject”, “individual” and “patient” are used interchangeably herein.

The sample is preferably an isolated sample obtained from a subject.

In one embodiment, the sample is typically selected from blood (e.g. a dried blood spot), plasma, saliva, serum, sputum, urine, cerebral spinal fluid, semen, cells, a cellular extract, a tissue sample, a tissue biopsy, a stool sample, a swab from any body site and/or one or more organs; typically blood, serum, urine, saliva and/or organ(s).

The term “blood” comprises whole blood, blood serum (henceforth “serum”) and blood plasma (henceforth “plasma”), preferably serum. Serum and plasma are derived from blood and thus may be considered as specific subtypes within the broader genus “blood”. Processes for obtaining serum or plasma from blood are known in the art. For example, it is known in the art that blood can be subjected to centrifugation in order to separate red blood cells, white blood cells, and plasma. Serum is defined as plasma that lacks clotting factors. Serum can be obtained by centrifugation of blood in which the clotting process has been triggered. Optionally, this can be carried out in specialised centrifuge tubes designed for this purpose.

In one embodiment, the sample is a dried blood spot (DBS). DBS samples comprise blood on a dry medium (such as paper). Blood from a DBS is isolated from the dry medium to provide a workable sample. Such isolation is typically referred to as elution, such that the resulting (workable) sample may be referred to as a “DBS eluate”.

In a particularly preferred embodiment, the sample is a DBS eluate.

A Dried blood spot testing (DBS) is a form of sample comprising blood blotted and dried on paper (preferably filter paper). Associated advantages include that the dried samples can easily be shipped to an analytical laboratory and analysed using various methods, notably a method of the invention.

Typically (“typically” not intended to be limiting), dried blood spot specimens are collected by applying a few drops of blood, drawn by lancet from the finger, heel or toe, onto specially manufactured absorbent filter paper. The blood is allowed to thoroughly saturate the paper and is air dried for several hours. Specimens can be stored in low gas-permeability plastic bags with desiccant added to reduce humidity, and may be kept at ambient temperature, even in tropical climates. Once in the laboratory, technicians can separate a small disc of saturated paper from the sheet using an automated or manual hole punch, e.g. dropping the disc into a flat bottomed microtitre plate. The blood is eluted out in buffer, preferably phosphate buffered saline which may contain 0.05% Tween 80 and 0.005% sodium azide, overnight at 4 °C. The resultant plate containing the eluates forms the "master" from which dilutions can be made for subsequent testing. As an alternative to punching out a paper disc, extraction of the sample by flushing an eluent through the filter without punching it out.

In one embodiment, the sample is blood (e.g. plasma or serum). For example, the sample may be EDTA plasma (e.g. plasma treated with Ethylenediaminetetraacetic acid, for example to provide an EDTA concentration of about 1.5mg/mL plasma). In a preferable embodiment, the sample is serum.

Additionally or alternatively, the sample may be an oral fluid sample, e.g. comprising saliva or sputum (preferably saliva).

In one embodiment, a sample may be processed to isolate an antibody from a sample.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 20 ED., John Wiley and Sons, New York (1994), and Hale & Marham, THE HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, NY (1991) provide the skilled person with a general dictionary of many of the terms used in this disclosure.

This disclosure is not limited by the exemplary methods and materials disclosed herein, and any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of this disclosure. Numeric ranges are inclusive of the numbers defining the range. Unless otherwise indicated, any nucleic acid sequences are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.

The headings provided herein are not limitations of the various aspects or embodiments of this disclosure.

Amino acids are referred to herein using the name of the amino acid, the three letter abbreviation or the single letter abbreviation. The term “protein", as used herein, includes proteins, polypeptides, and peptides. As used herein, the term “amino acid sequence” is synonymous with the term “polypeptide” and/or the term “protein”. In some instances, the term “amino acid sequence” is synonymous with the term “peptide”. In some instances, the term “amino acid sequence” is synonymous with the term “enzyme”. The terms "protein" and "polypeptide" are used interchangeably herein. In the present disclosure and claims, the conventional one-letter and three-letter codes for amino acid residues may be used. The 3- letter code for amino acids as defined in conformity with the IUPACIUB Joint Commission on Biochemical Nomenclature (JCBN). It is also understood that a polypeptide may be coded for by more than one nucleotide sequence due to the degeneracy of the genetic code.

Other definitions of terms may appear throughout the specification. Before the exemplary embodiments are described in more detail, it is to be understood that this disclosure is not limited to particular embodiments described, and as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be defined only by the appended claims.

Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limits of that range is also specifically disclosed. Each smaller range between any stated value or intervening value in a stated range and any other stated or intervening value in that stated range is encompassed within this disclosure. The upper and lower limits of these smaller ranges may independently be included or excluded in the range, and each range where either, neither or both limits are included in the smaller ranges is also encompassed within this disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in this disclosure. It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a compound” includes a plurality of such compounds and reference to “the position” includes reference to one or more positions and equivalents thereof known to those skilled in the art, and so forth.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that such publications constitute prior art to the claims appended hereto.

BRIEF DESCRIPTION OF THE DRAWINGS

Embodiments of the invention will now be described, by way of example only, with reference to the following Figures and Example.

Figure 1. Structures of SARS-CoV-2 spike-biliverdin (a, b) and spike-P008__056 Fab complexes, (a) Cryo-EM 3D reconstructions of trimeric SARS-CoV-2 spike ectodomain in 3RBD-down (left) and 1RBD-up (right) conformations determined under saturation with biliverdin. Biliverdin is encircled, glycans are present at various positions with one being pointed to with an arrow, (b) Details of the biliverdin binding pocket in the crystal structure. SARS-CoV-2 NTD is shown as cartoons with selected amino acid residues and biliverdin in sticks. Carbon atoms of the protein chain, sugars (NAG), and biliverdin have different shadings, biliverdin is encircled. Dark grey dashes are hydrogen bonds.

Figure 2. UV-visible light absorption spectral properties of coronaviral spike antigen constructs, (a) WT SARS-CoV-2 S1 protein (corresponding to viral spike residues 1-530, produced by transient expression in suspension-adapted human embryonic kidney cells): analysis of three independent batches by SDS PAGE (left) and spectra of four independent S1 batches (250-800 nm, right), (b-e) Spectra of stabilised trimeric SARS-CoV-2 spike ectodomain (residues 1-1208), NTD (1-310), RBD (319-541), and biliverdin (b); SARS-CoV-1 S1 (residues 1-518), HCoV NL63 S1 (residues 1-664) and OC43 S1 (1-665) (c); SARS-CoV- 2 S1 purified under acidic conditions in sodium acetate pH 5.2 or dialysed overnight against suspension of activated charcoal. Note the retention of biliverdin in dialysed sample, consistent with high affinity of the interaction at pH 8.0 ( ); H207A, R190K and N121Q SARS-CoV-2 S1 (e), compared to a representative spectrum of WT SARS-CoV-2 S1 purified under standard conditions, shows as black lines. Spectra were acquired from proteins diluted to 1-1.2 mg/ml (in 150 mM NaCI, 1 mM EDTA, 20 mM Hepes-NaOH, pH 8.0) and normalised to absorption at 278 nm.

Figure 3. Representative SPR sensorgrams (a-g) and melting point analysis (h). The sensorgrams were recorded with WT (a-e), R190K (f), or N121Q (g) SARS-CoV-2 S1. The proteins were immobilised on a sensor chip and binding and dissociation of biliverdin IXa (a, e-g), bilirubin (b), hemin (c), and protoporphyrin IX (d) was measured. The analytes were injected at indicated concentrations at pH 8.0 (a-d,f,g) or pH 5.0. Estimated KdS values are given in Table 1. Panel h shows melting behaviour of isolated SARS-CoV-2 NTD diluted to 30 mM in HBSE buffer (150 mM NaCI, 1 mM EDTA, 20 mM HEPES-NaOH, pH8.0) in the absence or presence of 100-1 ,000 mM biliverdin. The vertical axis corresponds to the first derivative of the ratios of fluorescence intensities measured at 350 and 330 nm wavelengths; the resulting melting points along with standard deviations (n=4) are given in the inset.

Figure 4. Multiple samples from 10 COVIDITY patients over 16 weeks - All patients were seropositive initially but became seronegative for at least one subsequent sample during the follow up period, on WT S1 DABA. Panel A shows those samples which measured S/CO < 0.7 on WT S1 DABA. X axis is S/CO value for Hybrid DABA. Upper panel denotes individual samples, black is S1 blue is Mutant S1 (a. a. 1-530 of S1, but with N121Q), line denotes the cut-off. Lower panels combine all samples. Asterix displays significance compared to S1 calculated with Wilcoxon matched-pairs signed rank test.

Figure 5. Multiple samples from 10 COVIDITY patients over 16 weeks - All patients were seropositive initially but became seronegative for at least one subsequent sample during the follow up period, on WT S1 DABA. Panel shows those samples which measured S/CO 0.7- 10 on WT S1 DABA. X axis is S/CO value for Hybrid DABA. Upper panels denote individual samples, black is S1 blue is Mutant S1, line denotes the cut-off. Lower panels combine all samples. Asterix displays significance compared to S1 calculated with Wilcoxon matched- pairs signed rank test.

Figure 6. Plots showing the follow up for 10 COVIDITY patients - All patients were seropositive initially but became seronegative for at least one subsequent sample during the follow up period, on WT S1 DABA. S1 in black, Mutant in blue. Plots highlighted in box no longer become seronegative when tested with Mutant S1. Figure 7. (A) Samples from NHS patients. Panel A shows those samples which measured S/CO < 0.7 on WT S1 DABA. X axis is S/CO value for Hybrid DABA. Left panels denote individual samples, black is S1, blue is Mutant S1, line denotes the cut-off. Right panels combine all samples. Asterix displays significance compared to S1 calculated with Wilcoxon matched-pairs signed rank test. (B) Samples from NHS patients. Panel B shows those samples which measured S/CO 0.7-5 on WT S1 DABA. X axis is S/CO value for Hybrid DABA. Left panels denote individual samples, black is S1, blue is Mutant S1 , line denotes the cut-off. Right panels combine all samples. Asterix displays significance compared to S1 calculated with Wilcoxon matched-pairs signed rank test. (C) Samples from NHS patients. Panel C shows those samples which measured S/CO >5 on WT S1 DABA. X axis is S/CO value for Hybrid DABA. Left panels denote individual samples, black is S1 , blue is Mutant S1, line denotes the cut-off. Right panels combine all samples. Asterix displays significance compared to S1 calculated with Wilcoxon matched-pairs signed rank test.

Figure 8. IgG capture assay results, from left to right, first box plot shows effect of removal of BLV from WT S1 (signals improve by 30%); second box plot shows effect of adding BLV back to WT S1 (signals go down), third box plot shows effect of adding BLV to Mut S1 (no negative effect), fourth box plot shows effect of mutation (Mutant - S1) - signals improve.

EXAMPLES

Materials and Methods

Protein expression and purification

DNA fragments encoding SARS-CoV-2 S1 (Uniprot ID: P0DTC2; residues 1-530), NTD (1- 310), RBD (319-541), SARS-CoV-1 S1 (Uniprot ID: P59594; residues 1-518), HCoV NL63 (Uniprot ID: Q6Q1S2; residues 1-618), HCoV OC43 (isolate LRTI_238, NCBI accession code KX344031 ; residues 1-619) were codon-optimised for expression in human cells and cloned into pQ-3C2xStrep vector under control of the cytomegalovirus (CMV) promoter for production of the recombinant proteins carrying a C-terminal extension containing human rhinovirus 14 3C protease recognition site followed by a TwinStrep tag. The signal peptide from immunoglobulin kappa gene product (METDTLLLWVLLLWVPGSTGD - SEQ ID NO.:5) was used to direct secretion of the RBD construct. The vector for production of the Hise- tagged stabilised trimeric SARS-CoV-2 has been described. Expression constructs encoding heavy and light chains of P008_056 Fab were made by inserting the respective coding sequences into pHLsec, including a sequence encoding a hexa-histidine (Hise) tag on the heavy chain fragment C-terminus. With exception of trimeric stabilized SARS-CoV-2 spike ectodomain, the proteins were produced by transient transfection of Expi293 (Thermo Fisher Scientific) cells with endotoxin- free preparations of the corresponding DNA constructs using ExpiFectamine293 (Thermo Fisher Scientific). The cells were maintained in shake flasks in FreeStyle293 (Thermo Fisher Scientific) medium at 37°C in humidified 5% CO2 atmosphere. To produce SARS-CoV-2 S1 NTD fragment for crystallography, cell culture medium was supplemented with 5 pM kifunensine (Sigma-Aldrich) to suppress complex glycosylation. Conditioned medium containing recombinant products was harvested twice, 4- and 8-days post-transfection, or once, for production of the NTD and P008_056 Fab, 5 days post-transfection. For production of the trimeric SARS-CoV-2 spike ectodomain, Expi293 transfected with the pcDNA3-based expression construct were selected with 250 pg/ml geneticin. Stably transfected cells, grown to a density of 3.5 million per ml at 37°C, were shifted to 32°C for 3 days prior to harvesting conditioned medium to enhance secretion of the viral glycoprotein.

TwinStrep-tagged proteins were captured on Strep-Tactin XT (I BA LifeSciences) affinity resin. Following extensive washes in TBSE (150 mM NaCI, 1 mM ethylenediaminetetraacetic acid (EDTA), 25 mM Tris-HCI, pH 8.0), the proteins were eluted in 1xBXT buffer (IBA LifeSciences). Hise-tagged proteins were captured on HisTrap Excel (Sigma-Aldrich) resin and eluted with 300 mM imidazole in phosphate buffered saline. For the use in crystallography, SARS-CoV-2 S1 NTD was digested with Endo Hf (New England Biolabs) and rhinoviral 3C protease to trim glycans and to remove the C-terminal twin Strep tag; Endo Hf was depleted by absorption to amylose resin (New England Biolabs). The proteins were further purified by size exclusion chromatography through a Superdex 200 16/600 column (GE Healthcare) in HBSE (150 mM NaCI, 1 mM EDTA, 20 mM Hepes-NaOH, pH 8.0) and concentrated by ultrafiltration using a Vivaspin-20 with 10-kDa cut-off (Sartorius). To deplete biliverdin from SARS-CoV-2 S1, recombinant protein eluted from Strep-Tactin XT resin was supplemented with 0.5 M sodium acetate, pH 5.2 and subjected to size exclusion chromatography through a Superdex 200 16/600 column in 200 mM sodium acetate, pH 5.2; fractions containing S1 were pooled and dialyzed overnight against HBSE buffer.

Surface Plasmon Resonance (SPR)

Experiments were performed on a Biacore S200 (GE Healthcare); S1 protein, diluted to 50 pg/ml in 10 mM sodium acetate, pH 5.0, was injected into a CM5 sensor chip (Cytiva product code BR100530) to achieve immobilisation to a level of 4,000 response units. Analyte binding was studied in running buffer comprising 150 mM NaCI, 50 mM HEPES- NaOH, pH 8.0 or 50 mM BisTris-HCI, pH 5.0, 0.05% Tween-20, and 1% dimethyl sulfoxide (DMSO). Biliverdin, bilirubin, haem, and protoporphyrin were obtained from Sigma-Aldrich (product codes 3089, 14370, 51280, and P8293, respectively). Generally, analyte stock solutions were prepared in DMSO prior to dilution in running buffer, maintaining the final DMSO concentration of 1%. The final analyte concentration was verified by spectrophotometry, using the following molar extinction coefficients: biliverdin 39,900 (at a wavelength of 388 nm), bilirubin 53,846 (460 nm), haem 58,440 (385 nm), and protoporphyrin IX 107,000 (407 nm). Alternatively, biliverdin, which is highly soluble at pH>7, was dissolved directly in running buffer, allowing to omit the solvent from the experiment. The presence of DMSO did not affect the observed Kd of S1 -biliverdin interaction (Table 1). All experiments were conducted using a CM5-kinetics-mutlicycle template at 25°C. Flow rate was 30 pl/min with a contact time of 180 s, followed by a dissociation time of 10 min; three start-ups were performed at the beginning of each experiment. Solvent correction was deemed unnecessary for the assays that contained DMSO. Biliverdin displayed very fast association. Data were analysed using the affinity software tool to calculate estimated Kd values in equilibrium regime.

Protein thermostability assay

Biliverdin-depleted SARS-CoV-2 NTD (corresponding to spike residues 1-310) was diluted to 1 mg/ml in 150 mM NaCI, 20 mM HEPES-NaOH, pH 8.0 and supplemented with biliverdin from a 5-mM stock prepared in 100 mM Tris-HCI, pH 8.0 where appropriate. Melting curves were recorded using 20-95 °C 1.5 °C/min temperature ramps on a Promethius NT.48 instrument (Nanotemper). Melting points were determined from inflection points of fluorescence intensity ratios (350 and 330 nm) using first derivative analysis.

Cryo-electron microscopy

Four pl stabilised trimeric SARS-CoV-2 spike ectodomain (0.6 mg/ml final concentration in TBSE supplemented with 0.1% n-octylglucoside) with 25 pM biliverdin or 0.2 mg/ml P008_056 Fab, was applied onto glow-discharged 200-mesh copper holey carbon R2/2 grids (Quantifoil) for 1 min, under 100% humidity at 20°C, before blotting for 3-4 sec and plungefreezing in liquid ethane using Vitrobot Mark IV (Thermo Fisher Scientific). The data were collected on Titan Krios microscopes operating at 300 keV (Thermo Fisher Scientific). Single particles of spike-biliverdin were imaged using a Falcon III direct electron detector (Thermo Fisher Scientific). A total of 15,962 movies were recorded with a calibrated pixel size of 1.09 A and a total electron exposure of 33 e'/A², spread over 30 frames in single electron counting mode. The spike-Fab complex was imaged on a GIF Quantum K2 detector with a post- column energy filter (Gatan), selecting a 20-eV window, in single electron counting mode. A total of 17,010 movies were collected with a pixel size of 1.38 A and total electron exposure of 51 e?A² spread over 40 frames. Both datasets were acquired with a defocus range of -1.6 to -4 pm (Table 2).

Crystal Structure of the NTD in complex with biliverdin

Protein construct (spanning SARS-CoV-2 S1 residues 1-310) at 10 mg/ml was supplemented with 90 pM biliverdin before mixing with crystallization mother liquor in a 1 :1 ratio. Plate-like crystals grew to 80-120 pm in two dimensions and -10-20 pm in the third dimension in conditions containing 24% PEG 3350 (w/v) and 0.25 M NaSCN by hanging drop vapour diffusion over 1-2 weeks at 18°C. Crystals were cryoprotected by the addition of PEG 400 to a final concentration of 30% (v/v) to the drop solution before flash freezing in liquid nitrogen.

X-ray diffraction data were collected at the PX1 beamline, Swiss Light Source, using wavelength 1 A, 100% transmission, a 40-pm beam, 0.1-sec exposure and 0.5° rotation per image. Data were indexed, scaled and merged using XDS and Aimless via Xia2. SARS-CoV- 2 spike NTD (residues 14-290; PDB ID 6ZGE) was used as a model for molecular replacement and yielded a solution containing one NTD per asymmetric unit, with a log likelihood gain of 490 and translation function Z-score of 22.7, in space group C222i using Phaser within the Phenix package. The initial molecular replacement solution was subjected to morph model in Phenix before commencing with rounds of manual fitting in Coot and refinement using phenix. refine, version 1.19rc4-4035. First, the protein chain was fitted and extended where possible, and refined, then glycosylation moieties were added where visualized in the positive Fo-Fc density, followed by conceivable PEG and water molecules. The electron density around the disulphide bonds suggested that they were labile and as such were modelled as alternative conformations between oxidized and reduced where appropriate and the occupancy refined between these states. The stability of the disulphide bonds could have been affected by trace amounts of DTT introduced during the treatment of the protein with 3C protease and EndoH. The Rf_ree and R_work were 21.5 and 18.5%, respectively, before a biliverdin molecule was fitted into the prominent positive difference density. The final refinement included four TLS groups (residues 14-67, 68-202, 203-278, 279-319) that had been segmented by the TLSMD server. All ligand geometry definition files were generated by Grade (Global Phasing) and model quality was assessed using Molprobity. The final model consists of spike residues 14-319, one biliverdin molecule, seven N-liked glycans (attached to asparagine residues at positions 17, 61 , 122, 149, 165, 234, and 282), 10 PEG moieties, and 351 water molecules and has reasonable geometry and fit to the electron density (Table 3). The model and the associated X-ray diffraction data were deposited with the Protein Data Bank under accession code 7B62.

IgG capture assay

In IgG capture assay experiments, the S1 construct used was amino acids 1-530 of the spike protein, with N121Q in the case of “mutant” S1. WT means this construct without substitution.

WT (depleted of biliverdin by chromatography under acidic conditions) and mutant SARS- CoV-2 S1 proteins (4.1 mg/ml; 100 pl) were conjugated to horse radish peroxidase (HRP) using the Lynx rapid HRP conjugation kit (BioRad). Following quenching and dilution in conjugate stabiliser (Clintech, Guildford, UK; product code #MI20080), half of each conjugate was supplemented with 10 pM biliverdin. Nunc 96-well, U8 MaxiSorp plates (Fisher Scientific) were coated overnight at 4°C with AffiniPure rabbit anti-human IgG antibody (Stratech; product code #309-005-008) diluted to 5 pg/ml in coating buffer (Clintech; product code #643005). Following a 3-h incubation at 37°C, and a 1-h incubation at room temperature, the wells were washed with washing buffer (Clintech; product code #20024) and incubated for 4 h in blocking solution (Clintech; product code #M 120011). The wells were air-dried and stored desiccated at 4°C until use. For ELISA, 100-pl serum samples, each diluted 1 :100 in diluent buffer (Clintech, product code #2040), were added to the coated wells and incubated stationary at 37°C for 1 h. To detect S1 -specific IgGs, the wells were washed with washing buffer (Clintech) and aspirated to dryness, following which 100 pl of S1-HRP fusion conjugate diluted in conjugate diluent (Clintech; product code #100171) to a previously defined optimum concentration (1 :1 ,500) were added and incubated for one hour at 37°C. The wells were then washed as before and developed for 30 min at 37°C using tetramethylbenzidine substrate (Clintech; product code #2030b), quenched by the addition of 50 pl stop solution (Clintech; product code #20031). The resulting optical densities (ODs) were acquired using a SpectraMax M2 reader (Molecular Devices).

The IgG capture ELISA data was modelled with a Bayesian linear model, using the gamma likelihood function: Gamma(p, Scale). The linear model took the form of log(p) = intercept[Sample] + offset[Protein], where the intercept[Sample] term allows varying intercepts across samples (to account for the repeated measurements), and the offset[Protein] term accounts for variation attributable to different protein coatings. Pairwise contrasts were drawn from the posterior distribution to construct credible intervals for the difference in OD values between different protein coatings. Monoclonal human antibodies

The following IgGs COVA1-26, COVA1-23, COVA2-38, COVA2-17, COVA1-20, COVA2-26, COVA1-22, COVA3-07, COVA2-03, COVA1-18, COVA1-12, COVA1-16, COVA2-01,

COVA2-02, COVA2-04, COVA2-07, COVA2-11, COVA2-15, COVA2-29, COVA2-39,

COVA2-44, COVA2-46, COVA2-10, COVA2-25, COVA2-30 have been reported (Science 07 Aug 2020: Vol. 369, Issue 6504, pp. 643-650, DOI: 10.1126/science.abc5902, incorporated herein by reference). Patients P003, P008 and P0054 were part of the COVID-IP study (Nature Medicine, volume 26, pages 1623-1635 (2020), incorporated herein by reference). Cloning and characterisation of human IgGs P008_056, P003_027, P008_039, P008_051, P008_052, P003_014, P008_057, P008_100, P008_081, P008_017, P008_087, P054_021, P008_007, P003_055, and P008_108 are described elsewhere.

ELISA with monoclonal IgGs

In ELISA experiments, the S1 construct used was amino acids 1-530 of the spike protein, with N121Q in the case of “mutant” S1. WT means this construct without substitution.

The assays were performed in a similar manner to the previously described protocol for serum samples. Briefly, high-binding ELISA plates (Corning, product code 3690) were coated with 3 pg/ml (25 pl per well) SARS-CoV2 WT S1 antigen (purified with or without acid treatment) or N121Q S1 in PBS, either overnight at 4 °C or for 2 h at 37 °C. Wells were washed with PBS supplemented with 0.05% Tween-20 (PBS-T) and blocked with 100 pl 2% casein in PBS for 1 h at room temperature. The wells were emptied and 25 pl of 2% casein in PBS was added per well. This solution was supplemented with biliverdin at 10 pM where indicated. Serial dilutions of IgGs were prepared in separate 96-well plate (Grenier Bio-one) in 2% casein, and then 25 pl of each serial dilution added to the ELISA assay plates and incubated for 2 h at room temperature. Wells were washed with PBS-T. Secondary antibody was added and incubated for 1 h at room temperature. IgG binding was detected using goat- anti-human-Fc conjugated to alkaline phosphatase (1 :1,000; Jackson, product code 109-055- 098). Wells were washed with PBS-T and alkaline phosphatase substrate (Sigma-Aldrich) was added and read at 405 nm. Area under the curve values were calculated using GraphPad Prism.

Double antigen bridging assay (DABA) assay

Test principle: The SARS-CoV-2 DABA is a three-step enzyme linked immunoassay that utilises a recombinant antigen pre-coated onto the polystyrene microwell solid phase, a second antigen of the same type, conjugated to the enzyme horseradish peroxidase (HRP), and a final enzyme reaction. In the first incubation, SARS-CoV-2 antibodies - if present - in the sample will be captured. Unspecific antibody is removed by the first wash step. Antibodies have more than one binding site, therefore the enzyme-conjugated antigen is able to bind to the captured antibody during the second incubation. Excess, unbound enzyme- conjugated antigen is removed in the second wash step. The presence of the antigen- antibody-antigen-enzyme immune complex is detected in the final step, an enzyme reaction. TMB Substrate is added to initiate this reaction. In the presence of peroxidase, TMB breaks down to form blue coloured products which change to yellow on adding the acid Stop Solution.

The yellow-coloured solution is measured using a photometric plate reader at 450 nm with background correction set between 620 and 650 nm. The presence of SARS-CoV-2 specific antibody is inferred by optical density values above the cut-off. The optical density is proportional to the amount of antibody present. Wells containing samples negative for RBD antibody remain colourless.

Immunoassay procedure: Instructions for the kit are as follows:

1. Remove and assemble the required number of microwell strips to perform the test. A minimum of 4 wells is needed for the controls which must be included in each test run. Return unused microwell strips and the desiccant to the foil pouch and reseal.

2. Pipette 50 pL of Sample Diluent into each well required.

3. Pipette 50 pL of the Positive Control (Reagent 4) and Negative Control (Reagent 5) to each assigned well, one well for the Positive Control and three (3) wells for the Negative Control.

Pipette 50 pL of each serum specimen to the assigned wells. Use a separate disposal pipette tip for each Sample, Negative Control and Positive Control to avoid cross contamination.

4. Place the microwell plate in a plastic bag (or else cover with lid or sealing tape) and mix gently by tapping the side of the plate strip holder.

5. Incubate at 37 ± 2°C in a moist chamber for 60 ± 2 minutes.

6. Wash wells five times with working strength Wash Buffer (see reagent preparation). The wash cycle is carried out as follows: aspirate the contents of the well and dispense 350 pL/well of diluted wash buffer, leave to soak for approximately 30 seconds and aspirate. Repeat the wash cycle four further times. It is recommended to use an automatic plate washer for this procedure. Tap the wells dry face down onto absorbent paper.

7. Dilute the stock conjugate (e.g. stock conjugate/ labelled antigen) into the volume of conjugate diluent required for the number of wells to be tested, to provide Working Strength Conjugate. Pipette 100 pL of Working Strength conjugate to each well, cover plate and incubate at 37 ± 2°C in a moist chamber for 60 ± 2 minutes.

8. Wash the wells five times with working strength Wash Buffer as in step 6.

9. Pipette 100 pL of TMB Substrate (Reagent 8) to each well. Incubate for 30 ± 2 minutes, protected from strong light at room temperature (18-25°C).

10. Pipette 100 pL of Stop Solution (Reagent 9) to each well.

11. Within 10 minutes, read the optical densities (OD) at 450 nm in an ELISA plate reader. If the feature is available, set the reference wavelength between 620 and 650 nm.

Quality control: The optical density OD450-620 nm of the Positive Control (PC) should be greater than 0.8 (preferably >1). The OD450-620 nm of each of the three Negative Control (NC) wells should less than 0.1.

Interpretation of the results: Calculate the mean OD of the three Negative Control wells (NCmean) . If one of the three OD values differs by more than 30% from the N Cmean, omit it and re-calculate the mean value.

The Cut-Off value for the assay is (NC mean + 0.10).

The following criteria are used for a specimen to be identified as SARS-COV-2 Antibody Reactive, Non-Reactive or Equivocal.

SARS-COV-2 Antibody Reactive: Specimen OD > (NC mean + 0.10) x 1.1

SARS-COV-2 Antibody Non-Reactive: Specimen OD < (NC mean + 0.10) x 0.9

Equivocal for SARS-COV-2 Antibody: (NC mean + 0.10) x 0.9 < Specimen OD < (NC mean + 0.10) x 1.1

A sample giving an equivocal result is re-tested. If the equivocal status cannot be resolved on re-testing, follow up samples taken between 7 and 21 days after the initial sample are tested in parallel with a further re-test of the first sample. If an equivocal result is obtained on re-testing a follow up sample, it is reported as SARS-COV-2 Antibody Non-Reactive.

To interpret results across plates, optical densities should be normalised using the Cut-Off value as below,

Binding Ratio = Specimen OD / Cut-Off In other words: each sample absorbance test OD result is valid if the Quality Control criteria are verified as below:

• The OD of each Negative Control must be less than 0.100

• The OD of blank must be less than 0.100

• The OD of each Positive Control should be greater than 0.8 (preferably >1.000)

Negative results (S/CO <1): Samples giving an OD less or equal to the cut-off value are considered negative, that is, no anti-SARS-CoV-2 RBD antibodies have been detected using this kit.

Positive results (S/CO >1): Samples giving OD greater than the cut-off value are positive for this assay, that is, antibodies to SARS-CoV-2 RBD have been detected.

Results are considered to be equivocal in the OD range 0.86 to 1.0. In these cases, samples are retested either by the same or by another assay and an explanation for the assay selected is provided.

EXAMPLES 1-4

Overview

The coronaviral spike glycoprotein is the dominant viral antigen and the target of neutralising antibodies. It is here shown that SARS-CoV-2 spike binds biliverdin, a tetrapyrrole product of haem metabolism, with nanomolar affinity in a pH-sensitive manner. Using cryo-electron microscopy and X-ray crystallography we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of NTD-specific neutralising antibodies. We show that access to the biliverdinsensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by biliverdin. Our results indicate that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope.

Trimeric coronaviral spike glycoproteins form prominent features on viral particles that are responsible for the attachment to a receptor on the host cell and, ultimately, fusion of the viral and cellular membranes. Encoded by a single viral gene, the mature spike glycoprotein comprises two subunits, S1 and S2, which mediate binding to the receptor and facilitate fusion, respectively. The recognition of the betacoronavirus SARS-CoV-2 host receptor, the cellular membrane protein angiotensin-converting enzyme 2, maps to the S1 C-terminal domain (referred to as the receptor binding domain, RBD), while the function of the N- terminal domain (NTD) remains enigmatic. Both S1 domains can be targeted by potent neutralising antibodies that arise in infected individuals. The majority of characterized neutralizing antibodies bind the RBD, while minimal structural information exists about neutralizing epitopes on the NTD.

Example 1 - S1 interacts with biliverdin

The immune properties of the spike glycoprotein underpin ongoing SARS-CoV-2 vaccine development efforts. Spike-derived antigens allow for specific detection of antibodies to SARS-CoV-2 on the background of recurrent infections with seasonal coronaviruses. In the course of our activities to support SARS-CoV-2 serology, we produced a range of recombinant coronaviral spike antigens by expression in human cell lines. Surprisingly, preparations of SARS-CoV-2 trimeric spike and S1 carried a distinct green hue, with prominent peaks at -390 and 670 nm in their light absorbance spectra (Fig. 2a). These unusual features were also evident in spectra of isolated SARS-CoV-2 S1 NTD, but not RBD (Fig 2b). In contrast, recombinant S1 constructs derived from the seasonal alphacoronavirus NL63 or the betacoronavirus OC43 did not absorb visible light (Fig. 2c). The spectra of SARS-CoV-2 spike constructs were consistent with biliverdin (Fig. 2b), a product of haem metabolism responsible for coloration of bruises and green jaundice. Biliverdin is produced at the first step of haem detoxification by oxygenases and is then reduced to bilirubin, the final product of tetrapyrrole catabolism in humans. We followed tetrapyrrole binding to immobilised SARS-CoV-2 S1 using surface plasmon resonance (SPR) and estimated the dissociation constant (Kd) for the interaction (biliverdin) at 9.8 ±1.3 nM (Fig. 3, Table 1). Bilirubin and haem bound S1 considerably more weakly, with apparent KdS of 720 ±240 nM and 6.9 ±1.2 pM, respectively, while no interaction was observed with protoporphyrin IX (Fig. 3, Table 1). Table 1. Affinity of SARS CoV2 S 1 interaction with tetrapyrroles measured using surface plasmon resonance.

¹Running buffer variables (DMSO and pH) are shown; full composition is given in Methods section.

BTP, BisTris Propane; BT, BisTris.

²Results of individual experiments performed in equilibrium mode.

³Mean and standard deviation shown for /V >2 measurements.

Example 2 - revealing structural basis for S1 -biliverdin interaction

Next, we imaged single particles of the trimeric SARS-CoV-2 spike ectodomain in the presence of excess biliverdin using cryo-electron microscopy. Image processing resulted in 3D reconstruction of closed (3RBDs-down) and partially open (1RBD-up conformation) states of the spike at 3.35 and 3.50 A resolution, respectively (Fig. 1a). Close inspection of the cryo- EM maps revealed features interpretable as a biliverdin molecule buried within a deep cleft on one side of each of the NTD domains (Fig. 1a). Unidentified entities at this position can be observed in prior cryo-EM reconstructions, presumably obtained with partial occupancy by the metabolite. To define the structural basis for the interaction more precisely, we cocrystallised the isolated NTD with biliverdin and determined the structure at 1.8 A resolution (Fig. 1b). The metabolite fits snugly into the cleft with the pyrrole rings B and C buried inside and propionate groups appended to rings A and D projecting toward the outside. The pocket is lined by hydrophobic residues (lle101, Trp104, Ile119, Val126, Met177, Phe192, Phe194, lle203, and Leu226), which form van der Waals interactions with the ligand. Biliverdin packs against His207, which projects its Ns2 atom towards pyrrolic amines, approaching three of them at ~3.6 A. Pyrroles A and B are involved in a 71-71 stacking with side chain of Arg190, which is stabilised by hydrogen bonding with Asn99. Ligand binding largely buries the side chain of Asn121 , which makes a hydrogen bond with the lactam group of pyrrole D. Example 3 - conservative substitution of amino acids in biliverdin binding pocket of S1 suppresses the interaction between S1 and biliverdin

The presence of a histidine residue in the biliverdin binding pocket suggested that the interaction may be pH-dependent. In agreement with this hypothesis, the Kd of the S1- biliverdin interaction increased to 250 ±100 pM at pH 5.0 (Fig. 3, Table 1), and purification under acidic conditions greatly diminished the biliverdin content of recombinant SARS-CoV-2 S1 (Fig. 2d). Substitutions of spike residues closely involved in ligand binding (H207A, R190K and N121Q) diminished pigmentation of purified recombinant protein (Fig. 2e). The biliverdin binding affinity of SARS-CoV-2 S1 was reduced by two and three orders of magnitude by the R190K and N121Q amino acid substitutions, respectively (Fig. 3, Table 1).

Example 4 - the structural basis for SARS-CoV-2 neutralisation by a biliverdinsensitive antibody

Access to the epitope is gated by a solvent-exposed loop composed of predominantly hydrophilic residues (“gate”, SARS-CoV-2 spike residues 174-188; Fig. 1). To allow antibody binding, it is believed the loop swings out of the way. The gating mechanism is controlled by insertion of Phe175 and Met177, which are located in the beginning of the loop, into the hydrophobic pocket vacated by biliverdin (Fig. 1). Antibody binding is additionally accompanied by an upward movement of a p-hairpin (“lip”, SARS-CoV-2 residues 143-155), which overlays a cluster of aromatic residues (Fig. 1).

Summary/ Discussion of Examples 1-4

It is well-established that viruses employ extensive glycosylation of their envelopes to shield antibody epitopes from recognition by humoral immunity, and -40% of SARS-CoV-2 spike surface is covered by glycans. Here, we identified and structurally characterised a novel class of a neutralizing epitope, present on SARS-CoV-2 S1, which is differentially exposed through recruitment of a metabolite. In contrast to glycosylation, co-opting a metabolite may allow conditional unmasking, for example under acidic conditions within the endosomal compartment. Biliverdin is the product of haem metabolism, and its concentration in the lung can be expected to drastically increase as Covid- 19 progresses to erythrocyte damage. Biliverdin levels in plasma of healthy individuals (0.9-6.9 pM) and more so under pathological conditions (>50 pM) greatly exceed the Kd of its interaction with the spike (-10 nM), and are therefore sufficient to affect SARS-CoV-2 antigenic properties and neutralisation. It would be of great interest to determine the levels of biliverdin and the related tetrapyrroles in lung tissue and how these may change during the course of mild versus severe disease. This is particularly important given the role of biliverdin in upregulating IL-10, one of the major markers of severe COVID-19. Finally, our results suggest that controlling biliverdin levels in vaccines and serological assay reagents may substantially alter outcomes.

EXAMPLES 5-6

Overview

It will now be demonstrated biliverdin binding masks the antigenic properties of the viral spike, which masking can be suppressed by conservative substitution of amino acids in biliverdin binding pocket of S1.

It is remarkable that a small molecule with a footprint of 370 A², corresponding to only -0.9% of solvent-exposed surface (per spike monomer), competes with a considerable fraction of spike-specific serum antibody population

In these experiments, the S1 construct used was amino acids 1-530 of the spike protein, with N121Q in the case of “mutant” S1. WT means this construct without substitution.

Example 5 - Mutation of amino acids in S1 biliverdin binding pocket leads to improved performance of S1 mutant in DABA assay

The S1 antigen was immobilised to the plate, and used to capture anti-SARS-CoV-2 serum antibodies. A horseradish peroxidase labelled RBD (amino acids 319-541 of the spike protein) was used to detect antibodies. The (immobilised) S1 construct used was amino acids 1-530 of the spike protein, with N121Q in the case of “mutant” S1. WT means this construct without substitution.

The mutant S1 was used as an immobilised capture antigen in a DABA assay (explained under materials and methods above, heading “Double antigen bridging assay (DABA) assay”).

Two sets of patient samples were used: COVIDITY samples (Figures 4-6); and NHS samples (Figures 7-8). The COVIDITY samples are 56 samples taken from 10 different patients across a 19 week period. All patients were seropositive initially, but all subsequently became seronegative on the standard S1 DABA (e.g. otherwise equivalent assay, but using non-mutated S1).

As can be seen from Figures 4-8, assay performance was improved with the mutant S1. Example 6 - Mutation of amino acids in S1 biliverdin binding pocket leads to improved performance of S1 mutant in IgG capture assay

Anti-human IgG antibody was immobilised on a plate, to which sample was applied (antibodies captured by said anti-human IgG). Labelled mutant S1 (else labelled corresponding non-mutated S1 amino acid residues 1-530 in control experiments, referred to as “WT”) was added. Unbound labelled antigen was washed, and anti-SARS-CoV-2 levels in sample quantified via signal from the labelled antigen (S1).

The data in the figures (see Figure 8) is presented showing differences in response to mutation and biliverdin (BLV) presence. Plotted are differences in signal (as % of signal, whiskers are at 10-90%):

• Effect of chemical removal of BLV from WT S1 (signals improve by 30%)

• Effect of adding BLV back to WT S1 (signals go down)

• Effect of adding BLV to Mut S1 (not much of an effect)

• Effect of mutation (Mutant - S1) (signals improve)

Data was first sorted to remove all sera which are negative by all S1 ELISA assays (sort by minimum value). Only data with S/CO 0.89 and above in at least one ELISA were used.

All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the present invention will be apparent to those skilled in the art without departing from the scope and spirit of the present invention. Although the present invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in biochemistry and biotechnology or related fields are intended to be within the scope of the following claims. SEQUENCES

Where an initial Met amino acid residue or a corresponding initial codon is indicated in any of the following SEQ ID NOs, said residue/codon is optional.

SEQ ID NO. 1 (the wild-type S1 subunit sequence of SARS-CoV-2 spike protein, NCBI Reference Sequence: YP 009724390.1)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNV TWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATN VVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN FKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGI YQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASF STFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAW NSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGF QPTNGVGYQPYRWVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVP VAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRR AR

SEQ ID NO. 2 (full sequence of SARS-CoV-2 spike protein, NCBI Reference Sequence: YP 009724390.1)

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNV TWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATN VVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGN FKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLT PGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGI YQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASF STFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAW NSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGF QPTNGVGYQPYRWVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKK FLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVP VAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRR

ARSVASQSI I AYTMSLGAENSVAYSN NSI Al PTN FTISVTTEI LPVSMTKTSVDCTMYICGDSTE CSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSK PSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTS ALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSL SSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRL QSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGWF LHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSG NCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASWNIQKEIDRLNE VAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCG SCCKFDEDDSEPVLKGVKLHYT

SEQ ID NO. 3 (amino acid residues 15-530 of the SARS-CoV-2 spike protein)

CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGT KRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDP FLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDG YFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAA AYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESI VRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLN

DLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNY

NYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRV VVLSFELLHAPATVCGPKKS

SEQ ID NO. 4 (amino acid residues 319-541 of the SARS-CoV-2 spike protein)

RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCY

GVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLD SKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGV

GYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF

SEQ ID NO. 5 (signal peptide)

METDTLLLWVLLLWVPGSTGD

Claims

58

1. A modified SARS-CoV spike protein S1 subunit (S1) polypeptide, having a modified amino acid sequence relative to a wild-type S1 sequence (SEQ ID NO: 1); a. the modified S1 polypeptide comprising at least one amino acid residue change located within a tetrapyrrole binding pocket for binding to a tetrapyrrole compound; b. wherein said at least one amino acid change is at a location on the modified S1 polypeptide sequence that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising: i. N99, 1101, W104, 1119, N121, V126, F175, M177, R190, F192, F194, I203, H207 and/or L226; and c. wherein the modified S1 polypeptide demonstrates lower binding affinity for said tetrapyrrole compound compared with wild-type S1.

2. The modified S1 polypeptide according to claim 1 , wherein the at least one amino acid change is at a location that corresponds to an amino acid location, of wild-type S1 (SEQ ID NO: 1), comprising N99, W104, 1119, N121, V126, F175, M177, R190, F192, H207 and/or L226.

3. The modified S1 polypeptide according to claim 1 or claim 2, wherein the at least one amino acid change is at a location that corresponds to an amino acid location, of wildtype S1 (SEQ ID NO: 1), comprising N121, R190, and/or H207.

4. The modified S1 polypeptide according to claim 1 , wherein the at least one amino acid residue change comprises: i. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N99 of the wild-type S1 (SEQ ID NO: 1); ii. an amino acid residue selected from the group consisting of glycine, alanine, valine, and leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1101 of the wild-type S1 (SEQ ID NO: 1); iii. an amino acid residue selected from the group consisting of phenylalanine, and tyrosine at the position on the modified S1 polypeptide 59 sequence that corresponds to amino acid residue W104 of the wild-type S1 (SEQ ID NO: 1); iv. an amino acid residue selected from the group consisting of glycine, alanine, valine, and leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue 1119 of the wild-type S1 (SEQ ID NO: 1); v. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); vi. an amino acid residue selected from the group consisting of glycine, alanine, and leucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue V126 of the wild-type S1 (SEQ ID NO: 1); vii. an amino acid residue selected from the group consisting of tyrosine and tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F175 of the wild-type S1 (SEQ ID NO: 1); viii. an amino acid residue selected from the group consisting of serine, cysteine, selenocysteine, and threonine, at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue M177 of the wild-type S1 (SEQ ID NO: 1); ix. an amino acid residue selected from the group consisting of a lysine and histidine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); x. an amino acid residue selected from the group consisting of tyrosine and tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F192 of the wild-type S1 (SEQ ID NO: 1); xi. an amino acid residue selected from the group consisting of tyrosine and tryptophan at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue F194 of the wild-type S1 (SEQ ID NO: 1); xii. an amino acid residue selected from the group consisting of glycine, alanine, valine, and leucine at the position on the modified S1 polypeptide 60 sequence that corresponds to amino acid residue I203 of the wild-type S1 (SEQ ID NO: 1); xiii. an amino acid residue selected from the group consisting of an alanine, lysine, arginine, glycine, valine, leucine and isoleucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1); and/or xiv. an amino acid residue selected from the group consisting of glycine, alanine, valine, isoleucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue L226 of the wild-type S1 (SEQ ID NO: 1). The modified S1 polypeptide according to any one of the preceding claims, wherein the at least one amino acid residue change comprises: i. an amino acid residue selected from the group consisting of glutamine, aspartate and glutamate at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); ii. an amino acid residue selected from the group consisting of a lysine and histidine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); and/or iii. an amino acid residue selected from the group consisting of an alanine, lysine, arginine, glycine, valine, leucine and isoleucine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1). The modified S1 polypeptide according to any one of the preceding claims, wherein the at least one amino acid residue change comprises: i. a glutamine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1); ii. a lysine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1); and/or 61 iii. an alanine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1).

7. The modified S1 polypeptide according to any one of claims 1-6, wherein the at least one amino acid residue change comprises: i. a glutamine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue N121 of the wild-type S1 (SEQ ID NO: 1).

8. The modified S1 polypeptide according to any one of claims 1-6, wherein the at least one amino acid residue change comprises: i. a lysine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue R190 of the wild-type S1 (SEQ ID NO: 1).

9. The modified S1 polypeptide according to any one of claims 1-6, wherein the at least one amino acid residue change comprises: i. an alanine at the position on the modified S1 polypeptide sequence that corresponds to amino acid residue H207 of the wild-type S1 (SEQ ID NO: 1).

10. The modified S1 according to claim any one of the preceding claims, wherein the modified S1 comprises or consists of a sequence corresponding to amino acid residues 15-530 of the SARS-CoV-2 spike protein S1 subunit (SEQ ID NO: 1), in which said at least one amino acid residue change is present.

11. A nucleic acid construct comprising or consisting of a nucleic acid sequence encoding the modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any preceding claim.

12. A host cell comprising the nucleic acid construct of claim 11.

13. A pseudotyped SARS-CoV virus, wherein the pseudotyped virus comprises a modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any one of claims 1-10. 62 An immunogenic composition comprising: a. the modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any of claims 1 to 10, or the nucleic acid construct of claim 11 , or the pseudotyped SARS-CoV virus as defined in claim 13; and b. a pharmaceutically acceptable carrier or excipient. An immunogenic composition according to claim 14 for use in preventing, treating or suppressing a SARS-CoV infection in a patient. An immunogenic composition according to claim 15 comprising the nucleic acid construct of claim 11 , for use in nucleic acid immunisation of a patient. A method for detecting the presence or absence of anti-SARS-CoV antibodies in a sample, the method comprising: a. contacting the sample with a solid-phase support having a first antigen immobilised thereto, i. wherein the first antigen comprises the modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any of claims 1 to 10; b. allowing anti-SARS-CoV antibodies present in the sample to bind to the modified S1 polypeptide, thereby forming a complex of modified S1 polypeptide and anti- SARS-CoV antibody; c. contacting said complex with a labelled second antigen, wherein said labelled second antigen comprises a SARS-CoV spike protein polypeptide (preferably wherein said labelled second antigen comprises or consists of a SARS-CoV receptor binding domain polypeptide, more preferably wherein said labelled second antigen comprises or consists of a sequence of SEQ ID No.: 4) that binds SARS-CoV antibody; d. allowing said labelled second antigen to bind to anti-SARS-CoV antibody present in the sample; e. removing labelled second antigen that is not bound to said complex; and f. detecting the presence of labelled second antigen bound to said complex; wherein the presence of labelled complex indicates the presence anti-SARS-CoV antibody in the sample, and wherein the absence of labelled complex indicates the absence of anti-SARS-CoV antibody in the sample.

18. A method for detecting the presence or absence of anti-SARS-CoV antibody in a sample, the method comprising: a. contacting the sample with a solid-phase support having anti-human IgG antibody and/ or anti-human IgM antibody immobilised thereon; b. allowing anti-SARS-CoV antibody (e.g. antibodies) present in the sample to bind to the immobilised anti-human IgG antibody and/ or anti-human IgM antibody, thereby forming an immobilised complex comprising said anti-human antibody and anti-SARS-CoV antibody; c. contacting said immobilised complex with a labelled antigen, i. wherein said labelled antigen comprises or consists of the modified SARS- CoV spike protein S1 subunit (S1) polypeptide as defined in any of claims 1 to 10, that binds anti-SARS-CoV antibody; d. allowing said labelled antigen to bind to anti-SARS-CoV antibody (e.g. antibodies) present in the immobilised complex; e. removing unbound labelled antigen; and f. detecting the presence of labelled antigen; wherein the presence of labelled antigen indicates the presence of anti-SARS-CoV antibody, and wherein the absence of labelled antigen indicates the absence of anti- SARS-CoV antibody.

19. The method according to any claim 17, wherein the labelled second antigen is amino acid residues 319-541 of the SARS-CoV-2 spike protein (SEQ ID NO.: 4) conjugated to a label.

20. The method according to any one of the preceding claims, wherein the labelled antigen is present in a fluid phase.

21. The method according to any one of claims 17-20, further comprising recording the output of said method on a data readable format.

22. An immunoassay solid-phase support for detecting the presence or absence of antibody to SARS-CoV in a sample, the solid-phase support comprising a first antigen immobilised thereto, a. wherein the first antigen comprises the modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any of claims 1 to 10. A kit for detecting the presence or absence of antibody to SARS-CoV in a sample, the kit comprising: a. an immunoassay solid-phase support as defined in claim 22, and b. a labelled second antigen, wherein said labelled second antigen comprises a SARS-CoV spike protein polypeptide (preferably wherein said labelled second antigen comprises or consists of a SARS-CoV receptor binding domain polypeptide, more preferably wherein said labelled second antigen comprises or consists of a sequence of SEQ ID No.: 4) that binds SARS-CoV antibody; optionally wherein the labelled second antigen is amino acid residues 319-541 of the SARS-CoV-2 spike protein (SEQ ID NO.: 4) conjugated to a label; or the kit comprising: c. a solid-phase support having anti-human IgG antibody and/ or anti-human IgM antibody immobilised thereon, wherein said anti-human IgG and IgM antibodies are able to capture and immobilise anti-SARS-CoV antibody in the sample; and d. a labelled antigen, wherein said labelled antigen comprises or consists of the modified SARS-CoV spike protein S1 subunit (S1) polypeptide as defined in any of claims 1 to 10, that binds anti-SARS-CoV antibody. The kit according to claim 23, further comprising instructions for use for detecting the presence or absence of antibody to SARS-CoV in a sample, preferably in a dried blood spot eluate sample. Use of a solid-phase support as defined in claim 22, or a kit as defined in claims 23 or 24, for detecting antibody to SARS-CoV in a sample. The modified S1, nucleic acid, host cell, pseudotyped virus, immunogenic composition, immunogenic composition for use, method, immunoassay solid-phase support, kit or use according to any one of the preceding claims, wherein the SARS-CoV is SARS-CoV-2.