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Design and fabrication of an aptamer-based biosensor for the detection of COVID-19
Thesis (MEng)--Stellenbosch University, 2024.
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| Format: | Thesis |
| Language: | en_ZA en_ZA |
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Stellenbosch : Stellenbosch University
2024
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| _version_ | 1867614099337117696 |
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| access_status_str | Open Access |
| author | Snyman, Dewald |
| author2 | Perold, Willem |
| author_browse | Perold, Willem Snyman, Dewald |
| author_facet | Perold, Willem Snyman, Dewald |
| author_sort | Snyman, Dewald |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MEng)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/130358 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA en_ZA |
| last_indexed | 2026-06-10T12:46:39.009Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/130358 Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 Snyman, Dewald Perold, Willem Sylvester, T. T. Stellenbosch University. Faculty of Engineering. Dept. of Electrical and Electronic Engineering. Medical electronics Pathogenic microorganisms -- Detection Aptamers COVID-19 (Disease) UCTD Thesis (MEng)--Stellenbosch University, 2024. ENGLISH ABSTRACT: Since the outbreak of COVID-19 and the recent exit from the state of a global pandemic, a lot of uncertainty still revolves around the detection and diagnosis of COVID-19. The reason for this is that since the initial outbreak there have been a multitude of detection methods implemented for the detection of COVID-19, however a lot of the methods suffer from disadvantages such as low accuracy and sensitivity. This lead to the practise where multiple methods are used during diagnosis. This can be a taxing procedure as these supplementary methods can be highly time consuming. This project will aim to implement a detection that is specific to COVID-19 that could potentially be used in a point-of-care testing scenarios. SARS-CoV-2 is spread through tiny droplets of viral particles from the respiratory tract through breathing, talking, sneezing, and coughing. Coronaviruses are potent in infecting human respiratory tracts causing problems such as pneumonia with symptoms including fever, cough, chills, myalgia, and diarrhoea. The SARS-CoV involved in the lower respiratory tracts can cause fatal pneumonia. The virus is a member of the Corona family, a complete coronavirus particle is made by the orchestrated formation of S, M, E, and N proteins to shape as the spherical structure. These structural proteins are the targets for the detection molecule for this project. The strategy used to develop the biosensor is built on the implementation of aptamers in a sensing environment. Aptamers are synthetic alternatives to antibodies that can be designed to bind with a specified target with high affinity. Through a thorough review and a supplementary study, the approach for the project was to use an electrochemical platform in conjunction with voltammetric transduction methods. Electrochemical platforms have been used in conjunction with aptamer for virus detections with low-cost and robust performance. The aptamers were immobilized on the sensing platform through the combination of a monolayer, covalent linkage and the streptavidin/biotin coupling. The monolayer was established through the use of DPA layer on the gold surface of electrodes, the layers is exposed to a EDC/NHS solution that will facilitate the covalent linkage with streptavidin. The acquired aptamers have biotinylated termini in it’s structure that is used to couple with the streptavidin bound to the sensor. The measurements and performance results of the sensor are obtained by voltammetric scans of CV and SWV with the use of a redox probe consisting out of ferricyanide/ferrocyanide and potassium chloride in phosphate-buffered saline. These scans provide peak current values that are used to access and evaluate the results and performance based on a signal-off redox approach. In order to implement these scans a potentiostat device is used, this device applies varying potentials according to different schemes and measures the current in order generate a sensor response. As part of the project a potentiostat was designed and developed so that all the experimental scans for the target detection can be executed on a home-built device. The measurements of the developed device is compared to the commercial device in order to evaluate the performance of the home-built device. All measurements for the sensor development and testing are first executed on the commercial device to verify the biosensor performance. All final detections and sensor development tests are still performed using the home-built device. The testing of the biosensor was conducted in two approach, plasma samples containing COVID-19 were injected into the developed sensor with the samples either injected directly or mixed with a PBS solution. The aptamer will bind to the structural proteins of the COVID molecule and successful detection will be indicated by decreased peak current values from the voltammetric scans. The project makes use of plasma samples from the blood of patients infected with COVID. Most of the tests that were conducted did yield a change in peak current values when the voltammetric scans were performed. This shows that the aptamers were able to bind to the COVID molecules, however in many of the measurements the decreased peak current values were larger then expected. This indicates that the aptamers are susceptible to non-spesific bindings, this was substantiate by the control samples tests where indications of binding was still present. The development and testing of the biosensor can still be regarded as a success even with diminished specificity. The voltammetric tests used for the final testing were performed with both the commercial potentiostat as well as the developed device. The commercial device did prove to be more sensitive to the electrochemical changes than the developed device. Both device were able to generate adequate results, however the developed device can still be improved especially with the filtering and smoothing of the accumulated data. The project as a whole can be regarded as a success as an electrochemical aptamer based biosensor was developed that was able to sens the presence of the target within a sample, alongside this the equipment used in conjunction with the sensor was also success developed, tested and demonstrated in the sensing scenario. The work done in this project can be deemed as a start to approaching a new streamlined and robust means of detecting COVID in a point-of-care application. AFRIKAANSE OPSOMMING: Met die uitbraak van COVID-19 en die onlangse eindiging van die wˆereld wye pandemie, is daar baie onsekerheid met betrekking to the waarneming en diagnose van COVID- 19. Die oorsaak van die onsekerheid is dat gedurende die pandemie was daar ’n groot verskeidenheid van metodes om COVID waar te neem. Die probleem was egter that baie van hierdie metodes was nie akkuraat of sensitief genoeg op hul eie nie. Dit het veroorsaak dat baie van hierdie metodes ondersteun or gepaard moet word deur een van die ander metodes om te verseker dat die diagnose korrek is. Hierdie is ’n langdraadige proses wat onnodige hulpbronne en tyd kan mors. Hierdie projek poog om dit te addresseer deur ’n metode van waarneming te implementeer wat die potensiaal kan hˆe om gebruik te work in versorgingpunt gevalle. SARS-CoV-2 versprei deur klein druppeltjies wat van die asemhalingskanaal af kom, dit kan plaasvind deur asmenhaling, gepraat, nies of gehoes. Coronavirusse is effektief met die infeksie van asemhalingskanale en kan probleme veroorsaak soos longontsteking met simptome insluitend koors, hoes, kouekoors en diarree. SARS-CoV kan doodelik wees indien die lae asemhalingskanaal aangetas word. Die virus is deel cna die Corona familie en die virus partikel se struktuur word geskep en bestaan uit verskeie struktuele prote¨iene naamliks die S, M, E en N prote¨iene. Hierdie struktuur prote¨iene is die teiken van hierdie projek. Die strategy wat die projek geimplementeer het maak gebruik van aptamers in ’n waarnemings toepassing. Aptamers is sintetiese alternatiewe molecule tot teenliggame wat ontwerp kan word om met ho¨e effektiwiteit met ’n spesifieke teiken te bind. Na die aflei van ’n studie was daar besluit op ’n strategie om die projek te voltooi, die sluit behels die gebruik van ’n elektrochemiese platform gepaard met voltammetriese metodes. Die elektrochemiese platform was al gebruik vir die waarneming van virusse asook met die implementering van aptamers. Die benadering vir hierdie projek kombineer oppervlak wysiging, kovalente binings en ’n direkte koppeling. Die oppervlak van goue electrode was aangepas met die blootstelling aan DPA om ’n laag te skep waarop die biosensor immobilisasie kan plaasvind. Met die combinasie van ’n EDC/NHS oplossing word die kovalente binding tussen die laag op die elektrode en streptavidin bewerkstellig. ’n direkte koppeling tussen streptavidin/Biotinylated aptamers word gebruik die aptamer op die oppervlak vas te vang. Alle biosensor ontwikkeling word ondersoek deur gebruik te maak can sikliese voltammetrie en viekantsgolf voltammetrie met ’n oplossing van ferrisianied/ferrosianied. Deur die verskillend piek reduksie en oksidasie stroom waardes te ondersoek kan met staaf of daar suksesvolle bindings plaasgevind het. Om die sikliese voltammetrie en viekantsgolf voltammetrie uit te voer was my eie weergawe van ’n potentiostaat ontwikkel. Die hardeware en sagteware vir die toestel was ontwerp, ontwikkel en getoets voor dit gebruk was vir enige biosensor waarnemings. Die ontwikkelde toestel was getoets deur sy waarnemings te vergelyk met ’n kommersiele toestel. Daarna is die ontwikklede potentiostaat betrokke by alle biosensor waarnemings en toetsfases. Nadat die biosensor en toepaslike hardeware ontwikkel is, is die sensor bloodgestel aan die teiken monster. Die teiken monster was bloed plasma vanaf patiente wat met COVID-19 besmet is. Meeste van die waarneimgs het getoon dat daar suksesvolle binding was met COVID. Die gevolgtrekking word geordersteun deur die afeneming van piek stroom waardes vanaf die sikliese voltammetrie en viekantsgolf voltammetrie. Die sensor het egter aan ’n probleem gelei van nie-spesifieke binding, met die gebruik van ’n kontrole monster was daar egter steeds ’n verander in piek stroom waardes waar die waardes bloot gehandhaaf moet word. Alhoewel hierdie ’n probleem is kan die toets en waarneming van die biosensor vir COVID steeds asa ’n sukses gesien word. Nadat die resultate ontleed is, kan die gestaaf word dat daar wel bindings plaasgevind het met COVID. Dit beteken at alhoewel die sensors in die projek steeds ’n paar tekortkominge bevat kan die stategie en benadring wat in die projek bebruik moontlik dien as ’n beginpunt vir die onwikkeling van ’n betroubare manier om COVID waar te neem. Masters 2024-02-28T07:49:29Z 2024-04-26T14:42:12Z 2024-02-28T07:49:29Z 2024-04-26T14:42:12Z 2024-03 Thesis https://scholar.sun.ac.za/handle/10019.1/130358 en_ZA en_ZA Stellenbosch University xviii, 389 pages : illustrations. application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Medical electronics Pathogenic microorganisms -- Detection Aptamers COVID-19 (Disease) UCTD Snyman, Dewald Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title | Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title_full | Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title_fullStr | Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title_full_unstemmed | Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title_short | Design and fabrication of an aptamer-based biosensor for the detection of COVID-19 |
| title_sort | design and fabrication of an aptamer based biosensor for the detection of covid 19 |
| topic | Medical electronics Pathogenic microorganisms -- Detection Aptamers COVID-19 (Disease) UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/130358 |
| work_keys_str_mv | AT snymandewald designandfabricationofanaptamerbasedbiosensorforthedetectionofcovid19 |