Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Abstract

Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.

Keywords: DNA/RNA extraction; Infectious diseases; Nucleic acid amplification; Plant diseases; Point-of-care diagnostics; Raw samples.

Graphical abstract

Fig. 1

Schematic illustrations of various microfluidic chips utilized for blood sample nucleic acid extraction: (a) PMMA microchip with two distinct regions for reagent storage and nucleic acid extraction (reproduced with permission from Ref (Zhang et al., 2019). © American Institute of Physics (AIP) 2019), (b) Surface-modified polyethylene terephthalate (PET) microchip for extraction of E. coli DNA from serum samples in 30 min (reproduced with permission from Ref (Choi et al., 2020)., © The Polymer Society of Korea and Springer (2019), (c) Cell lysis microchip for mixing whole blood and lysis buffer to lyse HIV-1 virus. (reproduced with permission from Ref. (Damhorst et al., 2015), © Engineering Sciences Press 2015), (d) Surface-modified micropillars-packed microchip for capturing E. coli cells from 50% whole blood (reproduced with permission from Ref (Hwang et al., 2011)., © Elsevier 2011), and (e) Dielectrophoresis chip for pathogen separation from diluted blood samples and PCR amplification (reproduced with permission from Ref. (Cai et al., 2014), © The Royal Society of Chemistry (2014).

Fig. 2

Various pump-free platforms for pathogen extraction and detection in blood. (a) The internal components of a portable centrifugal device developed for the extraction of HBV and E. coli DNA in 12 min (left), and a schematic diagram of target DNA extraction via laser irradiation (right) (reproduced with permission from Ref.(Cho et al., 2007), © The Royal Society of Chemistry © 2007). (b) Schematic of a centrifugal microfluid device showing the internal layout of various chambers used for sample preparation and nucleic acid amplification to detect HBV in 50 min (reproduced with permission from Ref. (L. Yang et al., 2018a, Yang et al., 2018b), © American Chemical Society 2019). (c) Schematic of a micropipette tip-based sample-to-answer E. coli detection system (reproduced with permission from Ref. (Lu et al., 2016), ©Elsevier 2016). (d) Schematic of a tube-based platform used for genomic DNA extraction from whole blood in 5 min (reproduced with permission from Ref. (Yin et al., 2019a), © The Royal Society of Chemistry (2019).

Fig. 3

Various paper-based devices used for nucleic acid extraction from human blood samples. (a) Cross section view and operating procedure of a sliding-strip device for E. coli detection in blood plasma (reproduced with permission from Ref. (Connelly et al., 2015), © American Chemical Society 2015). (b) Four-layered paper-based biosensor used to detect E. coli in blood, water and milk samples (left), and disposable tape used for sealing the paper device for LAMP amplification (right) (reproduced with permission from Ref. (Choi et al., 2016), © The Royal Society of Chemistry (2016). (c) Schematic of the interaction of charge-switchable chitosan and nucleic acid in a pH-dependent manner (reproduced with permission from Ref. (Byrnes et al., 2015), © The Royal Society of Chemistry (2015). (d) Operating process of a handheld, lateral flow device for extraction of S. aureus DNA from blood in 3 min (reproduced with permission from Ref. (Seok et al., 2019), © IOP Publishing 2019). (e) Schematic illustration of the working principle of a paper-strip device used for viral RNA extraction from serum sample (reproduced with permission from Ref. (Batule et al., 2020), © Elsevier 2020).

Fig. 4

Various portable devices used for nucleic acid extraction from human saliva samples. (a) Schematic of an integrated microfluidic cassette for detecting HIV-1 in saliva (reproduced with permission from Ref. (Chen et al., 2010), © Springer 2010). (b) Hybrid PDMS/aluminum oxide membrane/glass microchip used for S. aureus detection (top), and a cross section view of the chip (bottom) (reproduced with permission from Ref. (Oblath et al., 2013), © The Royal Society of Chemistry (2013). (c) Schematic illustration of an integrated molecular diagnostic system for tuberculosis detection from saliva in 45 min (reproduced with permission from Ref. (H. Yang et al., 2018), © Springer 2018). (d) 3D printer-based Zika virus detection platform (reproduced with permission from Ref. (Chan et al., 2018), © Elsevier 2018). (e) Paper-based Zika virus RNA extraction device (top), and operating mechanism of the ball valve used in the device (bottom) (reproduced with permission from Ref. (Jiang et al., 2018), © Willey Online Library 2018). (f) Schematic illustration of a Zika virus detection chip embedded with chitosan-modified capillaries to capture viral RNA from saliva (reproduced with permission from Ref. (Zhu et al., 2020), © MDPI 2020).

Fig. 5

Various sputum and oral swab sample preparation systems. (a) A handheld sputum collection device (reproduced with permission from Ref. (Park et al., 2018), © Springer Nature 2018). (b) 3D drawing of an integrated microfluidic cartridge used in tuberculosis detection, and a close-up image of the micropillar arrays utilized in SPE (inset) (reproduced with permission from Ref. (Wang et al., 2012), © Wiley Online Library 2012). (c) Tube-based automatic nucleic acid extraction and amplification system for M. tb detection (reproduced with permission from Ref. (Creecy et al., 2015), © PLoS One 2015). (d) Schematic layout of a centrifugal microfluidic device showing various chambers for DNA extraction and amplification for tuberculosis detection in 2 h (reproduced with permission from Ref. (Loo et al., 2017), © Elsevier 2017). (e) Paper microfluidic origami device for sputum sample preparation (reproduced with permission from Ref. (Govindarajan et al., 2012), © The Royal Society of Chemistry (2012). (f) Schematic diagram of an integrated microchip used in pneumoniae detection (left), and a photograph of the microchip (right) (reproduced with permission from Ref (Wang et al., 2019)., © Elsevier 2019).

Fig. 6

Various microfluidic devices utilized to isolate nucleic acids from nasal specimens. (a) Schematic and photograph of an integrated microchip used in whooping cough detection. Yellow, red, green, and blue dyes indicate the domains for nucleic acid extraction, amplification, injection, and amplicon separation, respectively (reproduced with permission from Ref. (Easley et al., 2006), © PNAS 2006). (b) Microfluidic chip attached with two thin-film heaters for continuous flow PCR amplification to detect Influenza A virus (reproduced with permission from Ref. (Cao et al., 2012), © PLoS One 2012). (c) Images of a microfluidic cassette used for the extraction of viral and bacterial nucleic acid from nasal swab (top) and a portable controlling unit (bottom) (reproduced with permission from Ref. (Van Heirstraeten et al., 2014), © The Royal Society of Chemistry (2014). (d) A PES membrane-based paper device filtering RNA-Glycoblue precipitate from cell lysate for H1N1 detection (top), and schematic illustrations of the paper device (bottom) (reproduced with permission from Ref. (Rodriguez et al., 2015), © American Chemical Society 2015). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7

Various portable urine sample preparation systems. (a) DMA-based nucleic acid extraction in an amine-modified silicon microchip (reproduced with permission from Ref (Shin et al., 2014)., © The Royal Society of Chemistry (2014). (b) Schematic of a high-gradient magnetic separation (HGMS) enabled nucleic acid extraction method (reproduced with permission from Ref. (Pearlman et al., 2020), © American Chemical Society 2020). (c) Schematic illustration of a chromatography paper-based nucleic acid extraction system for Chlamydia trachomatis detection (reproduced with permission from Ref (Linnes et al., 2014)., © The Royal Society of Chemistry (2014). (d) Schematic of the microfluidic filtration of small Zika RNA in a wax-printed cellulose paper (reproduced with permission from Ref (Kaarj et al., 2018)., © Springer Nature 2018). (e) A pipette-actuated capillary comb system for sample-to-answer bacterial pathogen detection in 85 min. Cross section view of the system (top left), actual photographs (top right), schematic of liquid handling through the system (bottom left), and a photograph of the assembled capillary comb and 1 mL pipette tip (bottom right) (reproduced with permission from Ref (Hui et al., 2018)., © The Royal Society of Chemistry (2018). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 8

Rapid nucleic acid extraction methods from plant samples. (a) Photograph of an Agdia sample preparation bag with ground leaves inside (reproduced with permission from Ref (McCoy et al., 2020)., © MDPI 2020). (b) FTA card-based sample preparation. Pressing of infected leaves onto FTA card (left) and punching a small FTA disk for subsequent molecular analysis (right). (reproduced with permission from Ref. (Ndunguru et al., 2005), © BioMed Central 2005). (c) Photograph of a cellulose dipstick (left), and schematic illustration of the dipstick based nucleic acid purification from ground leaf sample (right) (reproduced with permission from Ref (Zou et al., 2017)., ©PLoS Biology 2017). (d) Schematic illustration of microneedle patch-based nucleic acid extraction method (reproduced with permission from Ref (Paul et al., 2019)., © American Chemical Society 2019).