DNA Aptamer Gold Nanoparticle Colorimetric Diagnostic Test Kit of Saliva Samples for SARS_Cov2 Virus Linked to Mobile Phone Application (Aptamex™)
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Abstract
The development of the use of DNA aptamers for clinical applications to detect human diseases is at the forefront of research. Synthetic DNA aptamers are easy to generate, inexpensive, highly specific and have been postulated to replace antibodies for research and clinical use. Despite the considerable amount of published work on the use of DNA aptamers for research use, to date they have not been exploited for clinical diagnostics. SARS-CoV-2 virus is a pandemic causing a global disruptive event preventing people from travel, work and leisure activities resulting in a major health crisis, hospital overloads and a high death rate. The detection of SARS-CoV-2 virus in communities is therefore very important, especially for returning normality of life. The current gold standard for detection of SARS-CoV-2 virus is RT-PCR, a technique that is relatively expensive and most importantly with a slow turnaround time between sample procurement and result. This paper describes the development of a rapid, accurate, low-cost, facile to use assay for the detection of the SARS-CoV-2 spike protein in saliva. The assay exploits a simple system based on the use of a gold nanoparticle-aptamer complex, that can be easily produced and distributed, facilitating its deployment to the point-of-need, potentially reaching millions of individuals in resource-limited settings. The proposed colorimetric diagnostic test kit uses a SARS-CoV-2 DNA aptamer adsorbed on gold nanoparticles and salt-induced aggregation to detect the presence of SARS-CoV-2 Spike protein in saliva samples indicated by a color change of the gold absorbance spectrum that can be quantified by a spectrophotometer, linked to a mobile phone for data processing and analysis. The assay parameters were optimized and then tested in a field calibration clinical test in Indonesia. At a research level, a limit of detection of ca. 1.25 nM to synthetic spike protein (S1) was observed and a method to test human saliva samples developed. The DNA aptamer was specific to SARS-CoV-2, with minor cross-reactivity observed with MERS and SARS-CoV-1, but negligible cross-reactivity seen with common cold coronaviruses. A calibration clinical test of patients in Indonesia demonstrated a classification resulting in a > 97% sensitivity and a > 97% specificity compared with saliva RT-PCR test for SARS-CoV-2. Furthermore, the data indicates that anatomical location and sample type (swab vs saliva) can affect RT-PCR results. In conclusion, we have developed the use of a robust and reproducible aptamer-gold nanoparticle assay for clinical diagnostic use based on a colorimetric system that is cheap, simple, rapid, sensitive and can be employed for large scale testing of human populations for SARS-CoV-2 virus.
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SciScore for 10.1101/2022.02.09.22269224: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Participants for Calibration test in patients: Work flow: Following patient information and consent to participate in the study, the patient is asked to fast from food and drink for at least 30 minutes. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources When the patient has fasted for at least 30 minutes, the first saliva sample is collected according to the protocol of either QuickSpit or BioSaliva. BioSalivasuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when …
SciScore for 10.1101/2022.02.09.22269224: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: Participants for Calibration test in patients: Work flow: Following patient information and consent to participate in the study, the patient is asked to fast from food and drink for at least 30 minutes. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources When the patient has fasted for at least 30 minutes, the first saliva sample is collected according to the protocol of either QuickSpit or BioSaliva. BioSalivasuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:A single test gives an answer at a single point in time and cannot be the basis of re-opening businesses and in controlling the pandemic, suggesting that testing should be frequent, carried out at least twice a week, in order to make these rapid tests effective in a pandemic [26-29], thus highlighting the critical requirement for a cheap, easy-to-use, rapid, robust assay, which can be facilely manufactured and deployed to all countries, independent of the local resource limitations. An important advantage of the AptameX™ assay is that it does not depend on components used in lateral flow based rapid antigen tests, such as membranes, conjugate pads, sample pads, plastic cassettes, which are now in huge demand, with the test simply requiring gold nanoparticles, DNA and NaCl, reagents which are widely available from a plethora of suppliers worldwide. The performance of antigen-based rapid diagnostic tests varies greatly with clinical sensitivities ranging from 23% - 71% and 2-5 orders of magnitude less sensitive than RT-PCR [26-29]. Current rapid tests have high sensitivities at CT values of 25 or lower, but at higher CT values particularly above 28, performance declines [26-29]. Optimal CT values should be lower than 25. A case in point: the example where Innova tests “identified only two-thirds of the cases with CT levels below 25” indicates that the laboratory which processed the samples performed at a level far from what should be required. Their CT value of 25 would probabl...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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