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Sample-to-answer paper-basednucleic acid amplification tests

Time: Fri 2022-11-25 14.00

Location: Kollegiesalen, Brinellvägen 8, Stockholm

Language: English

Subject area: Fibre and Polymer Science

Doctoral student: Georgios Chondrogiannis , Fiberteknologi, KTH Royal Institute of Technology

Opponent: Associate Professor Keith Pardee, University of Toronto

Supervisor: Universitetslektor Mahiar Hamedi, Fiberteknologi; Doktor Jeff Mold,

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QC 2022-11-03


Nucleic Acid Amplification Tests (NAATs) with PCR technology to amplify DNA, are the golden standard for infectious disease diagnostics, but they require benchtop instruments and trained users to be performed. For this reason, we all had to send PCR test to centralized laboratories during the Covid-19 pandemic. A year into the pandemic, home-based antigen paper-based tests became available for Covid, but these were not as sensitive, so PCR tests had to be used still. This development emphasized the need for technologies that enable NAATs with superior sensitivity to be performed at home. There are three technological advanced that could make such tests possible: 1)  Paper based devices, called paper microfluidics, have been developed to enable more advanced steps of testing without laboratory equipment. These paper-based system incorporate advanced functionality and multiple reaction steps. 2) New DNA amplification techniques, called isothermal amplification, have been developed which, contrary to PCR, can be run without a thermocycler, enabling DNA amplification to be carried out even inside a paper.  3) Several methods to detect DNA have been shown using paper.

One step that is still largely unsolved in NAATs is the sample preparation step, hindering the development of fully paper-based NAATs. In sample preparation, nucleic acids are extracted from bacteria or virus, usually using reagents harmful to DNA amplification. These steps are thereofore complicated and require several washing steps and heating, and are therefore difficult to integrate into paper.

In this thesis, we used a simple, cost-effective, and scalable method to incorporate sample preparation in paper, thus taking NAATs towards point of care. We solve this problem by immobilizing enzymes that are used for sample preparation on nitrocellulose paper. The immobilized enzymes remain functional and can be used for biochemical reactions, while they are strongly bound to the paper. This method enables the separation of these enzymes from the sample, protecting downstream sensitive reactions of DNA amplification and eliminates the need for high temperature deactivation or washing steps. Specifically, we show that the enzyme achromopeptidase can do cell lysis from the Staphylococcus epidermidis bacteria, a common pathogenic gram-positive bacterium, and use its DNA in further reaction to perform a sample-to-answer paper-based NAAT. These NAATs employed a low temperature amplification step called Recombinase Polymerase Amplification (RPA) and DNA detection with a lateral flow strip.

We further show the enzyme proteinase K, also immobilized on paper, can digest RNase in saliva samples, an enzyme that breaks down RNA leading to false-negative results. This results enabled an easy sample preparation step towards saliva viral DNA self-testing.

Finally, in this work we developed a paper microfluidic system that can carry out an enzyme-linked oligonucleotide assay, which demonstrated much higher sensitivity in detecting amplified DNA than conventional lateral flow assays. In summary, these results provide solutions towards high-performing, affordable and instrument-free paper-based NAATs home-testing.