AptameX is the lead product of a DNA aptamer platform technology with the objective of developing transformational diagnostics for the world. Unique, innovative technology that addresses the need for frequent mass testing, AptameX is the solution to return communities into safe places during this pandemic. Gain insight into a highly accurate and sensitive technology that will revolutionise rapid testing and assist in many facets of living and moving about in a smart way within a Covid environment.
AptameX is a DNA aptamer gold nanoparticle diagnostic test for Covid-19 that is fast, accurate, and cost-effective. AptameX involves a synthetic single-strand DNA aptamer that targets the S1 spike protein on the surface of SARS-CoV-2. The diagnostic takes 15 minutes to complete and is for professional use only.
Aptamer: from Latin, aptus meaning “to fit” and meros meaning “part”
Aptamers are short, single-stranded DNA or RNA (ssDNA or ssRNA) that can selectively bind a specific target molecule such as proteins, peptides, carbohydrates, small molecules, toxins and even live cells. Aptamers fit their targets .
- They bind their targets with high selectivity and specificity.
- The binding is determined by its tertiary structure because they tend to form helices and single-stranded loops.
- An aptamer recognises and binds its target through shape-dependent, 3D interactions, but also hydrophobic interactions, base-stacking and intercalation.
Base-stacking: the 3D arrangement of bases in nucleic acids. By stacking, the hydrogen bonds formed lead to structural stability.
Intercalation: the insertion of molecules between the planar DNA bases.
In the case of AptameX, an ssDNA aptamer binds the spike glycoprotein (S1) of the SARS-CoV-2 virus.
Aptamer Selection by SELEX
Aptamer selection against a particular target molecule is done by SELEX, Sequential Evolution of Ligands by Exponential Enrichment. It involves a large oligonucleotide library in an iterative process where non-binders are eliminated from the process and binders are subjected to multiple rounds where selectivity is enhanced. The SELEX process is illustrated below .
Also called colloidal gold, a colloidal suspension of nanoparticles of gold, usually in water. Gold nanoparticles range from an intense red colour to blue/purple to clear and colourless. The red hue is attributed to spherical particles under 100 nm; the blue, to larger spheres or nanorods; and colourless, to larger particles. Ultimately, colour is dependent on particle size, shape, local refractive index and aggregation state. Their optical, electronic, and molecular-recognition properties lend themselves to wide range of applications including nanotechnology, materials science, and medical technology .
Aptamer – AuNP Mode of Action
Refer to the explanation below.
- DNA aptamers are conjugated to gold nanoparticles
- Upon binding between the S1 virus glycoprotein and the aptamer, gold nanoparticles are released
- When gold nanoparticles are released, they aggregate causing a spectrochemical color change in the solution
- Colorimetric assay: spectrophotometer detects the colour change
- Software developed to analyse the colour change (shift in visible spectra) designates positive or negative results.
Representative spectra of naked gold nanoparticles, aptamer conjugated to gold nanoparticles, and displaced and aggregated gold nanoparticles are shown below.
Interpreting the spectra of the gold nanoparticles with respect to binding of the aptamer to the S1 viral protein is the principle of AptameX as a Covid-19 diagnostic test. Achiko AG, in commercialising the technology, has developed the software to analyse the above phenomenon associated with gold nanoparticles to transform the technology into a rapid, diagnostic test.
The software algorithm assesses the shape of the curve (i.e., the Signal) derived from the spectral shift, and:
- The result is negative if the algorithm determines that the Signal is within limit of the negative control.
- The result is positive if the algorithm determines that the Signal has shifted: different wavelength maxima, different slopes along the curve, etc.
- If the Signal is in between the allowed limits of positive and negative, the result is inconclusive.
- If the Signal is well outside the expected values for positive and negative results, the result is invalid and the sample may be re-tested.
With the use of multiple data processing methods (i.e., derivatives, modals, ratios), quantitative patterns within the spectral absorbance data were analysed and examined for correlations across classified datasets versus PCR results, Negative and Positive Controls. Data models were developed and optimised by having the least variance from established experimental control data. The software algorithm was developed empirically from over a hundred cases. The more tests are run, the better results can be classified .
Distribution curve of viral load over time
The viral load over the course of a COVID infection is illustrated by the distribution curve below.
The following observations can be made from the graph above:
- Peak viral load in the upper respiratory tract: from symptom onset to 10 days after
- Viral load in week 1 is significantly higher than in week 2, yet infectivity is still critical
- Asymptomatic and pre-symptomatic persons may be transmitting virus
- PCR: most sensitive test, viral RNA is amplified but requires expensive equipment and hours to process samples
- Less sensitive rapid antigen tests have a higher limit of detection and will miss a substantial fraction of infected patients
- AptameX is a more sensitive test and positions itself “where rapid tests need to be”, i.e., closer to the performance of RT-PCR.
Infectiousness and the testing landscape
The degree of infectiousness is related to cultivable virus. RT-PCR detection can serve a proxy to understand infectiousness since there is a strong correlation of Ct value with the degree of cultivable virus. This in turn provides an understanding of the effectiveness of COVID diagnostic tests.
** A geometric mean is an average that indicates the central value of a set of numbers that is exponential in nature or where the values are meant to be multiplied.
- Ct ≤ 25 : enzyme-based rapid antigen tests have sensitivities > 80%
- Ct > 35 : viral loads are very low; a person is likely not contagious 
- Ct = 28.3 : AptameX sensitivity is 77.6% 
- Higher sensitivity than average rapid antigen test (see below)
- Able to identify more people who are infectious
- Suitable for frequent, mass testing
AptameX’s sensitivity was determined at Ct ~ 28 where peak testing performance is needed (see Geometric Mean above).
Sensitivity of Rapid Tests
Antigen tests tend to have high sensitivity at high viral loads but at low viral loads, their sensitivities drop over a wide range. Their performance start to decrease from a Ct value of 28.
The graphical representation above is corroborated by the actual sensitivities at specific Ct values in the table below [8,9].
- Base Pair Biotechnologies, Inc. “What is an Aptamer? – Aptamers and SELEX” https://www.basepairbio.com/what-is-an-aptamer/
- L.A. Dykman and N.G. Khlebtsov. “Gold Nanoparticles in Biology and Medicine: Recent Advances and Prospects” in Acta Naturae. 2011 Apr-Jun; 3(2): 34–55. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347577/
- Bartolomeo Della Ventura et al. “Colorimetric Test for Fast Detection of SARS-CoV‐2 in Nasal and Throat Swabs” in ACS Sens. 2020, 5, 3043−3048. https://pubs.acs.org/doi/abs/10.1021/acssensors.0c01742
- Anika Singanayagam, et al. “Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020.” in Euro Surveill. 2020;25(32): pii=2001483. https://doi.org/10.2807/1560-7917.ES.2020.25.32.2001483; https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.32.2001483
- Epimonitor. “Special Recap: Going From A to Z On Coronavirus With Anthony Fauci—A Unique Interview Conducted By Fellow Scientists.” http://www.epimonitor.net/Fauci-Interview.htm
- Georgia Guglielmi. “Rapid Coronavirus Tests: A Guide for the Perplexed” in Nature, Vol. 590, 11 February 2021, pp. 202-205. https://www.nature.com/articles/d41586-021-00332-4
- Gannon CK Mak, et al. “Analytical sensitivity and clinical sensitivity of the three rapid antigen detection kits for detection of SARS-CoV-2 virus,” Journal of Clinical Virology 133 (2020) 104684. https://doi.org/10.1016/j.jcv.2020.104684; https://www.sciencedirect.com/science/article/abs/pii/S1386653220304261?via%3Dihub
- Gannon CK Mak, et al. Evaluation of rapid antigen detection kit from the WHO Emergency Use List for detecting SARS-CoV-2 Journal of Clinical Virology 134 (2021) 104712. https://doi.org/10.1016/j.jcv.2020.104712; https://linkinghub.elsevier.com/retrieve/pii/S1386653220304546