Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review

Zhang, Mengyao; Ye, Jing; He, Jinsong; Zhang, Fang; Ping, Jianfeng; Qian, Cheng; Wu, Jian

doi:10.1016/j.aca.2019.11.056

Cited by 98 publications

(69 citation statements)

References 119 publications

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“…Several miniatured sample preparation techniques for whole blood, plasma, or serum have been reported for POC pathogen detection ( Batule et al, 2020 ; Ganguli et al, 2017 ; L. Zhang et al, 2020a , Zhang et al, 2020b ), short tandem repeat analysis ( Gan et al, 2014 ; Lounsbury et al, 2013 ), single nucleotide polymorphism detection ( Lu et al, 2016 ), cancer diagnosis ( Zhang et al, 2010 ), forensic analysis ( Duarte et al, 2010 ), and hereditary genetic testing ( Zhuang et al, 2015 ). However, rapid sample preparation platforms for forensic analysis are beyond the scope of this review.…”

Section: Nucleic Acid Extraction From Human Bloodmentioning

confidence: 99%

“… Sample Type Target Pathogen Cell Lysis Method Nucleic Acid Extraction Technique Nucleic Acid Amplification Method LOD Total Sample-To-Answer/Sample Preparation Time Reference Rhododendron plant Leaves Phytophthora Species Agdia sample extraction bag RPA using lyophilized RPA reagents 33 pg DNA/reaction 30 min (sample-to-answer) McCoy et al (2020) Rice leaf Magnaporthe oryzae Chemical lysis with SDS based buffer Cellulose-based dipstick captured DNA from lysate RPA 3 min (sample preparation) (Y. Zhang et al, 2020a , Zhang et al, 2020b ) Pinewood chips Bursaphelenchus xylophilus Quick DAP extraction buffer RPA using lyophilized TwistAmp RPA kit (TwistDX, UK) 6 pg DNA/reaction 30 min (sample-to-answer) Cha et al (2020) Plant leaves and woods Xylella fastidiosa, Ceratocystis platani and Phytophthora ramorum OptiGene Plant Material Lysis Kit Real-time LAMP 0.02 pg/μL DNA 20 min (sample-to-answer) Aglietti et al (2019) Tomato, eggplant and cucumber (fruit) Phytophthora nicotianae Water extraction method Real-time LAMP 10 fg DNA/reaction 20 min (sample-to-answer) Hieno et al (2019) Tomato leaves Phytophthora infestans Mic...…”

Section: Nucleic Acid Extraction From Plantsmentioning

confidence: 99%

“…In addition to FTA cards, cellulose-based papers such as Whatman No.1 paper (GE Healthcare, USA) have also been reported for DNA purification from crude cell lysate (Y. Zhang et al, 2020a , Zhang et al, 2020b ; Zou et al, 2017 ). Zou et al (2017) presented a cellulose dipstick-based nucleic acid purification system for several plants, including rice, tomato, wheat, soybean, barley, and sugarcane ( Fig.…”

Section: Nucleic Acid Extraction From Plantsmentioning

confidence: 99%

“…Smartphone-based nucleic acid detection platforms have been used for rapid screening of both human and plant diseases in resource-limited settings ( Hernández-Neuta et al, 2019 ; Kong et al, 2017 ). Finally, the LAMP assay can also be detected and quantified by turbidity or color change of the assay solution ( Curtis et al, 2008 ; Estrela et al, 2019 ; M. Zhang et al, 2020a , Zhang et al, 2020b ). For colorimetric detection of the LAMP assay, pH-sensitive dyes ( Kaarj et al, 2018 ), metal ion indicators ( Port et al, 2014 ; Seok et al, 2017 ), or functionalized gold nanoparticles ( Choi et al, 2016 ) have been reported as color indicators in the literature.…”

Section: Introductionmentioning

confidence: 99%

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

Paul

Ostermann

Wei

2020

Biosensors and Bioelectronics

134

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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.

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Section: Nucleic Acid Extraction From Human Bloodmentioning

confidence: 99%

Section: Nucleic Acid Extraction From Plantsmentioning

confidence: 99%

Section: Nucleic Acid Extraction From Plantsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Paul

Ostermann

Wei

2020

Biosensors and Bioelectronics

134

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show abstract

“…The nucleic acid-based techniques aim to detect the specific nucleic acid sequence by amplifying the target sequence to millions of folds. They usually provide more timely and accurate results compared with traditional immunoassays and culturing methods [12]. The study of Torresi et al [13] applied a specific real-time PCR screening assay designed for the rapid identification of Listeria monocytogenes strains potentially related to the outbreaks occurred in Central Italy from January 2015 to March 2016.…”

mentioning

confidence: 99%

Rapid Methods for Assessing Food Safety and Quality

Visciano

Schirone

2020

Foods

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Food safety represents a central issue for the global food chain and a daily concern for all people. Contaminated food by physical, biological or chemical hazards can harm consumers, increasing demand for health services, government expenditure on public health and other social costs. The quality assurance programs are based on the continuous monitoring of raw matter, production process, storage and distribution of the end products, including the purpose for which they are intended. Such programs represent an important objective for food producers, not only for the potential risk to human health, but also for the economic losses to which they can be subjected. The development and use of rapid analytical methods able to identify the main failures in food production can benefit food companies by saving time and costs for the good and fast control of products through the entire food chain.

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Establishment and evaluation of a new fluorescent probe method based on loop‐mediated isothermal amplification for the detection of Mycobacterium tuberculosis complex

Batuer,

Yuan,

et al. 2024

Luminescence

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We aimed to develop a novel diagnostic method called multiplex fluorescence of loop primer upon self‐dequenching loop‐mediated isothermal amplification (mFLOS‐LAMP) for the rapid detection of Mycobacterium tuberculosis complex (MTBC). A set of specific primers was designed to target the detection of IS1081 and IS6110 genes, which are insertion sequences within the MTBC. The 110 sputum specimens collected were assessed using the established mFLOS‐LAMP method, multiplex polymerase chain reaction, Xpert MTB/RIF, and smear microscopy. The optimal reaction temperature and duration for mFLOS‐LAMP were determined to be 65°C and 30 min, respectively, by optimizing the entire system. The detection sensitivity of mFLOS‐LAMP was 6.0 × 101 CFU/mL, by Bacillus Calmette‐Guerin, and the mFLOS‐LAMP sensitivity of M. tuberculosis H37Rv genomic DNA was 500 fg, and the specificity was 100%. The sensitivity of mFLOS‐LAMP was 94.2% and the specificity was 96.6%, when Xpert MTB/RIF was used as the reference method. There was no statistically significant difference in their detection rate (χ2 = 0, P = 1.000), and the consistency was good (kappa = 0.909, P < 0.001). The receiver operating characteristic analysis yielded the maximum area under the curve of 0.954. The mFLOS‐LAMP method demonstrated high sensitivity and specificity, allowing for swift and accurate detection of MTBC.

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Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review

Cited by 98 publications

References 119 publications

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

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

Rapid Methods for Assessing Food Safety and Quality

Establishment and evaluation of a new fluorescent probe method based on loop‐mediated isothermal amplification for the detection of Mycobacterium tuberculosis complex

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