Improved methods for point of care detection of blood-borne pathogens

• Main Author: Kolluri, Nikunja
• Other Authors: Klapperich, Catherine M.
• Language: en_US
• Published: 2020
• Subjects: Biomedical engineering; Diagnostics; DNA/RNA extraction; HIV; Isothermal; Malaria; Point of care
• Online Access: https://hdl.handle.net/2144/41024

Preventing the spread of blood-borne infectious diseases is vital to improving global health outcomes, particularly for low- and middle-income countries (LMICs). Sensitive and accurate diagnosis of infections is vital to this effort. Nucleic acid amplification tests (NAATs), which amplify pathogen nucleic acids, are gold-standard techniques for detection and quantification of pathogen levels. However, standard NAATs such as polymerase chain reaction (PCR) require expensive equipment for blood sample processing and DNA/RNA amplification, making them challenging to implement in resource-limited areas of LMICs. In this work, I developed two methods to simplify sample processing and amplification to make NAATs more accessible for use at the point of care in resource-limited areas of LMICs. The first method enables instrument-free nucleic acid extraction from whole blood. A room temperature lysis chemistry and a paper-and-plastic sample capture device were developed to isolate, purify, and store pathogen DNA and RNA on a paper capture membrane. Extracted nucleic acids can be eluted and used in standard NAATs or in developmental amplification assays. I demonstrated successful isolation of HIV virion RNA and P. falciparum parasite DNA from whole blood samples over several concentrations with >60% recovery. Extracted RNA remains stable on the capture membrane for two weeks at room temperature and 37°C, alleviating the need for cold storage after sample collection. These results are a promising step toward using this method for simplified sample extraction and storage in low-resource settings in LMICs. The second method I developed is a novel isothermal amplification technique for P. falciparum DNA. Sensitive diagnosis of P. falciparum infection is vital to identify and treat low-density, asymptomatic infections and move closer to eliminating malaria. Highly sensitive PCR assays are difficult to deploy in resource-limited areas of LMICs and existing isothermal methods require complex assay design and are often not sensitive enough to diagnose asymptomatic infections. Here, I developed a novel isothermal technique which amplifies multiple regions of the P. falciparum genome, generating a large amount of DNA for better analytical sensitivity. The assay achieves a lower limit of detection of ~23.4 fg P. falciparum gDNA/µL (~1 parasite/µL) in 30 minutes, similar gold-standard PCR assay while using a fraction of the resources required for PCR. Lastly, I adapted the assay for implementation at the point of care. I showed that the assay directly amplifies P. falciparum parasite DNA captured on paper with the paper-and-plastic device previously developed. I also incorporated visual assay readout with lateral flow strips, eliminating the need for specialized equipment to detect amplified DNA. I explored methods to eliminate cold storage of reagents by stabilizing amplification enzymes at room temperature. The work described in this thesis represents two enhanced methods for point of care detection of blood borne pathogens. By simplifying sample extraction, amplification, and detection, the methods described here make NAATs more accessible to low-resource areas of LMICs. The whole blood nucleic acid extraction device and isothermal assay described in this work can be used together for sensitive diagnosis of P. falciparum malaria. The methods can also be used independently, or in combination with other techniques routinely used in the field. The flexibility built in to these methods enables easier integration into existing workflows in LMICs. === 2021-05-18T00:00:00Z