COVID-19 Molecular Testing in Korea: Practical Essentials and Answers From Experts Based on Experiences of Emergency Use Authorization Assays
2020; 40(6): 439-447
Ann Lab Med 2021; 41(6): 549-558
Published online November 1, 2021 https://doi.org/10.3343/alm.2021.41.6.549
Copyright © Korean Society for Laboratory Medicine.
1Department of Chemical Pathology and NHLS- Tshwane Academic Division, University of Pretoria, Pretoria, South Africa; 2Division of Chemical Pathology, University of Cape Town, Cape Town, South Africa; 3Department of Chemical Pathology, University of Pretoria, Prinshof Campus, Pretoria, South Africa; 4Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; 5Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, China
Correspondence to: Tahir S. Pillay, MBChB., Ph.D.
Department of Chemical Pathology,
University of Pretoria, Prinshof Campus, Arcadia, Pretoria, 0007, South Africa
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Antibodies have proven to be central in the development of diagnostic methods over decades, moving from polyclonal antibodies to the milestone development of monoclonal antibodies. Although monoclonal antibodies play a valuable role in diagnosis, their production is technically demanding and can be expensive. The large size of monoclonal antibodies (150 kDa) makes their re-engineering using recombinant methods a challenge. Single-domain antibodies, such as “nanobodies,” are a relatively new class of diagnostic probes that originated serendipitously during the assay of camel serum. The immune system of the camelid family (camels, llamas, and alpacas) has evolved uniquely to produce heavy-chain antibodies that contain a single monomeric variable antibody domain in a smaller functional unit of 12–15 kDa. Interestingly, the same biological phenomenon is observed in sharks. Since a single-domain antibody molecule is smaller than a conventional mammalian antibody, recombinant engineering and protein expression in vitro using bacterial production systems are much simpler. The entire gene encoding such an antibody can be cloned and expressed in vitro. Single-domain antibodies are very stable and heat-resistant, and hence do not require cold storage, especially when incorporated into a diagnostic kit. Their simple genetic structure allows easy re-engineering of the protein to introduce new antigen-binding characteristics or attach labels. Here, we review the applications of single-domain antibodies in laboratory diagnosis and discuss the future potential in this area.
Keywords: Single-domain antibodies, Nanobodies, Monoclonal antibodies, Laboratory diagnosis
Ligand binding assays are fundamental in laboratory medicine for measuring analytes and biomarkers. This class of assays exploits the binding reaction between an analyte or biomarker and a specific affinity reagent. In immunoassays, the affinity reagent is an antibody.
Immunoassays form the mainstay for protein biomarker measurements, and numerous proteins can be measured in healthy and diseased states. Some target proteins are abundantly present (>10 mg/mL), whereas others are found at very low concentrations (<1 pg/mL) in clinical samples. The development of a suitable immunoassay depends on the availability of the protein antigen and the generation of an immune response in the host animal and the subsequent production of antibodies. Owing to the inherent diversity of an immune response and the structure and binding affinity of different antibodies for the same antigen, antibodies used in one assay or platform behave differently from those used in another, unless they are the same clone of monoclonal antibody. There are numerous examples of variable results between different platforms for the same analyte, such as thyroid stimulating hormone and cancer antigen 19-9 [1, 2]. Post-translational modifications of a protein analyte might be another factor that could affect reactivity with an antibody and lead to variable results. The challenges of using conventional antibodies in the laboratory have been outlined by Goodman .
However, there are many problems with immunoassays. In general, antibodies can originate from polyclonal or monoclonal sources. Although they are easy to produce, polyclonal antibodies are variable by nature, and there can be batch-to-batch variations in sera. Polyclonal antibodies have the advantage of being able to recognize multiple epitopes of a complex antigen, but inconsistency in production has hindered their use. The development of monoclonal antibodies was a milestone in the evolution of ligand-based assays. Monoclonal antibodies recognize a single epitope and can be produced in a pure and homogeneous form indefinitely from a hybridoma. Although monoclonal antibodies have a valuable role in diagnosis, their production is technically demanding and can be expensive. Moreover, the size of monoclonal antibodies (150 kDa) makes their re-engineering using recombinant methods a challenge. There is thus a need to develop new robust and reliable antibody probes for laboratory diagnosis. Conventional antibodies or complementary nucleic acid sequences represent the most common form of probes for the detection of various target molecules. Through the years, there have been attempts to reduce antibodies into fragments, either via enzymatic digestion methods (e.g., using pepsin or papain) or via recombinant engineering methods, such as those employing fragment antigen binding (Fab), single chain variable fragment (ScFv), and fragment variable (Fv) . The discovery of naturally occurring heavy chain-only antibodies (HCAbs) in camelids heralded a new era in antibody engineering [5, 6].
The classical/canonical antibody in vertebrates contains two identical heavy and two identical light chains (Fig. 1). The immune system of camelids (camels, dromedaries, llamas, guanacos, vicuñas, and alpacas) has evolved uniquely to produce dimeric HCAb of approximately 90 kDa that lack light chains and the CH1 domain (the first constant heavy chain domain) (Fig. 1). Among mammals, only members of the Camelidae family produce endogenous functional heavy-chain-only IgG. Interestingly, a similar biological phenomenon is observed in sharks [6, 7]. Cartilaginous fish, including nurse (
The serendipitous discovery of the natural occurrence of the unique, functional, homodimeric, HCIg in camelid serum resulted from a laboratory course for graduate students at the Vrije Universiteit Brussels, Belgium . Unlike the canonical mammalian antibody, HCIg contains a single intact antigen-binding domain (variable domain of heavy chain of HCIg, VHH). The counterpart to the VHH in cartilaginous fish is variable domain of IgNAR (V-NAR). This single-domain fragment contains only two hypervariable loop structures participating in antigen binding, whereas the VHH contains three hypervariable loops for antigen recognition. It has been postulated that the absence of the CH1 in these HCIgs resulted from the loss of a splice consensus signal at the 5´ end of the “CH1-hinge” intron during evolution [8, 9]. This altered splicing results in the joining of the CH2 domain of HCAb to the variable domain through a “hinge” region, which is unique to this class of antibodies .
There are two distinct types of hinges in the heavy chain-only IgG of camelids: the short hinge and the long hinge [5, 10]. The VHH resembles conventional VH domains but is distinct in sequence and structure in that its sequence contains a few critical amino acid substitutions in the region that normally interacts with the variable light chain domain (VL) [5, 11-14]. These substitutions of large hydrophobic amino acids (in VH) with smaller, hydrophilic amino acids (in VHH) are responsible for the soluble behavior of the VHH and its function in the absence of a VL partner.
Thus, these variable antigen-binding domains (VHH and V-NAR) are fully functional within a small 12–15 kDa unit . The VHH contains approximately 120 amino acid residues, encoded by a gene of 360 bp. This gene can be cloned and subcloned easily. A protein size of approximately 13 kDa is well within the limits of bacterial expression and is comparable with ScFv (25 kDa), Fab fragments (57 kDa), and the intact IgG (150 kDa).
VHH molecules form the basis to generate small, recombinant, autonomous single-domain antigen-binding fragments. The term “nanobody” was coined by the company Ablynx (Ghent, Belgium) in 2003 as a trademark, but it is now being generally used to describe small, recombinant, autonomous single-domain antigen-binding proteins, because of their small size (13 kDa; 2.5 nm in diameter and 4 nm in length). These nanobodies comprise a relatively new class of diagnostic probes. The patent on the use of fragments derived from the HCAb originally filed by Vrije Universiteit Brussel expired in 2014, resulting in increased interest in the commercialization of nanobodies .
The process of generating nanobodies begins with the immunization of a camelid. Following the development of an immune response, B-lymphocytes are isolated either from the peripheral blood or from lymph nodes and used to isolate mRNA. The mRNA is then used in reverse transcription to produce cDNA and perform PCR with VHH-specific primers to amplify the VHH gene region, which is then cloned into a phage display expression vector to generate a library. Only primers for VHH are required, as opposed to the entire HCIg, because VHH alone contains the fully functional antigen-binding domain of the HCIg.
The process of animal immunization can also be bypassed through the construction of a naive or synthetic cDNA library. Thus, it is also possible to obtain VHHs from non-immune libraries , but immune libraries have greater diversity and usually yield VHHs with higher affinities . Reactive VHHs that might bind weakly to the target can be modified by random or site-directed mutagenesis to isolate higher affinity binders.
Using the solid phase immobilized protein antigen (e.g., on magnetic beads), phage-expressing reactive nanobodies can be isolated through repeated cycles of screening and amplification in bacterial culture. Phage inserts can then be subcloned into bacterial or yeast expression vectors. The
A typical nanobody has affinities (equilibrium dissociation constant) in the nanomolar to picomolar range, making them highly suited for application in ligand-binding assays . They can bind to antigens with comparable affinity to that of conventional IgG, even though they lack the light chains that make up the antigen-binding region in IgG . Since the functional part of the entire nanobody molecule is smaller than that of a conventional mammalian antibody, recombinant engineering and protein expression
Low cost of production: the small size of nanobodies enables easier production and high yields in moderate volumes of bacterial culture. Expression can be periplasmic or cytoplasmic. Periplasmic expression allows disulfide bridges to form and the purification of proteins from periplasmic extracts at yields of 1–20 mg/L on average . Cytoplasmic expression produces much higher yields at 60–200 mg/L.
Easy tailoring to meet the application requirements (i.e., to improve specificity and affinity for broadening detection possibilities): the genes encoding nanobodies can be easily re-engineered to select for altered binding properties or epitope tagging for an immunoassay configuration. Single-domain antibodies bind to targets with comparable affinity to that of many conventional antibodies, sometimes with dissociation constants in the low picomolar range . A myriad of methods is available to increase the affinity or avidity of any given nanobody. The availability of cDNA for a particular nanobody allows easy insertion of protein tags or labels using standard recombination methods.
Robustness and long shelf live: nanobodies are exceptionally heat stable in comparison with Igs and ScFv fragments and can thus be easily shipped at most ambient temperatures [18, 23]. Their melting temperatures (Tm) can be as high as 80°C, and some can be engineered to have a Tm of even up to 90°C. Some VHHs, but not all, can refold and renature to 100% after denaturation.
Targeting cryptic or hidden epitopes: the small size of a nanobody allows it to enter antigen-binding sites in protein pockets and cavities that might not be accessible to conventional antibodies . VHHs can bind to a variety of epitopes, from enzyme active sites [25, 26] to small molecules or haptens [27, 28].
Low immunogenicity [29, 30] and rapid blood clearance: the small size of a nanobody allows it to be freely filtered in the glomerulus, facilitating excretion. Therefore, for non-invasive in vivo imaging or therapeutic applications, if a nanobody is tagged with an anti-cancer molecule, residual toxicity will be minimized as the nanobody gets excreted. Nanobodies have low immunogenicity due to their sequence similarity with human IgG .
The average affinity of a nanobody for its antigen is approximately 6 nM, which is comparable with the affinity of the monomeric antigen-binding sites (Fab or ScFv) of conventional antibodies for their antigens . The structures of numerous nanobodies have been revealed by X-ray crystallography . VHH contains an IgV fold with nine β-strands and a conserved disulfide bond between Cys23 and Cys104 (International ImMunoGeneTics [IMGT] information system numbering; Fig. 2). The V domain contains three hypervariable loops linked by four conserved framework regions. The paratopes on nanobodies are enriched with aromatic residues similar to conventional antibodies. The interactions between nanobodies and antigens are mediated by the three complementarity-determining region (CDR) loops and dominated by the CDR3 loop. The antigen epitopes tend to be more rigid and concave and are also enriched with aromatic residues. In contrast, conventional antibodies use six CDR loops (three in the variable domain of the heavy chain and three in the variable domain of the light chain) for antigen binding . These structural insights are instrumental for the rational-design engineering of nanobodies into more potent affinity reagents .
The question regarding which immunoassay applications benefit most from the substitution of classical antibodies with nanobodies remains. Nanobodies have been introduced in a wide variety of laboratory diagnostic techniques, mainly those for infectious diseases (Table 1). Considering their low cost of production and robust behavior (thermoresistance, long shelf life even in the absence of a cold chain), nanobodies are expected to become a preferred affinity reagent in future affordable LFAs. Nanobodies are perhaps less applicable for the “pregnancy test” type of applications but more applicable to assays that are used to monitor infectious diseases in animals (both farm and wild-life animals) living in remote areas. Efforts were made to monitor trypanosome and dengue fever using nanobodies [34, 35].The lack of applicability to techniques, such as a pregnancy/HCG detection test, relates to the long-established footprint of conventional monoclonal antibody usage, and investment in HCG detection will make it difficult for nanobodies to replace monoclonal antibodies for these techniques.
In addition to LFAs, nanobodies have been assessed for the detection of various targets in ELISA-based methods. Although the generation of nanobodies against haptens is challenging, nanobodies against multiple small organic compounds have been identified [27, 36-39]. These nanobodies, combined with sensitive detection technologies or in competitive ELISA formats, appear to be a valuable tool for monitoring contaminants in soil or on food. For this, first, contaminating herbicides, fungicides, or insecticides must be extracted from soil or food. Many of these contaminants are hydrophobic and poorly soluble in aqueous solutions, and their extraction in dimethyl sulfoxide, methanol, acetone, and other organic solvents is not compatible with the proteinaceous probes. However, stable nanobodies appear to be resistant to exposure to such non-physiological solutes [40-42].
The diagnostic sensitivities of LFAs and standard sandwich ELISA for particularly difficult-to-measure targets (i.e., glycosylated, biomarkers involved in variable assemblies or when present at extremely low concentrations), seem to be inadequate. In such cases, it might be necessary to switch to more sensitive detection methods, such as CLEIA or BLEIA, or more sophisticated new diagnostic instruments, such as (magneto-) electrochemical sensors [39, 43, 44]. The flexible format and small size of nanobodies allows for tailoring and adaptation for directional coupling at a high density on magnetic beads or on the sensor layer of novel biosensors [45, 46]. For example, the prostate specific antigen (PSA) sandwich immunosensor has a detection limit of 0.08 ng/mL and range of 0.1–100 ng/mL while the surface plasmon resonance assay for PSA has a detection limit of 0.3 ng/mL, well below the clinical-detection lower limit of 4 ng/mL [45, 46]. This contrasts with the higher detection limits of various automated platforms using conventional antibodies . Similar advantages in sensitivity were seen with a growth hormone assay utilizing a nanobody, wherein a detection range of 0.5–110 ng/mL was achieved . Our efforts to design better performing assays culminated in a recent highly reproducible sensitive and specific assay for Toxocara excretory secretory components [49, 50].
Although many efforts have been undertaken in academic institutions to introduce nanobodies in standard ELISAs to monitor biomarkers for human health (Table 1), it will be extremely difficult to substitute the well-established classical monoclonal antibodies in these applications (refer to the HCG test example). Nevertheless, there might be one notable exception, specifically
Pillay TS conceived the idea for the review article and produced the first draft. Muyldermans S reviewed and modified the first draft extensively for the final submission.
Funding was provided by the National Research Foundation, South Africa.