Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms
Abstract
:1. Introduction
2. Loop-Mediated Isothermal Amplification
2.1. Principle of LAMP for RNA Virus Detection
2.2. Applications of LAMP for RNA Virus Detection
2.2.1. Fluorescence-Based Detection Methods
2.2.2. Colorimetric-Based Detection Method
2.2.3. Others Detection Methods
3. Recombinase Polymerase Amplification
3.1. Principle of RPA
3.2. Applications of RPA for RNA Virus Detection
3.2.1. Fluorescence-Based Detection Methods
3.2.2. Colorimetric-Based Detection Methods
4. Recombinase-Aided Amplification
4.1. Principle of RAA
4.2. Applications of RAA for Virus Detection
5. Other Isothermal Amplification-Based Platforms for RNA Virus Detection
5.1. Nucleic Acid Sequence-Based Amplification
5.2. Helicase-Dependent Amplification
6. Commercialized Isothermal Amplification Devices for SARS-CoV-2 Detection
7. Limitations and Future Perspectives on Isothermal Amplification Methods
7.1. Recent Challenges of Isothermal Amplification Techniques
7.2. Future Perspectives
8. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Type of Virus | Target | Sample | Detection Methods | Limit of Detection (LOD) | Time (min) | Temperature (°C) | Ref. |
---|---|---|---|---|---|---|---|
Ebola virus | ssRNA (−) | Cell culture | Nucleic acid strip detection (NAD) | 30 copies/mL | 35 | 58 | [24] |
African swine fever virus | dsRNA | Tissue | CRISPR-Cas12a nuclease reaction | 7 copies/μL | 30 | 37 | [25] |
HIV | ssRNA-RT | Plasma sample | CY5 channel fluorescence | 89 copies/reaction | 50 | 64 | [26] |
Tomato brown rugose fruit virus | ssRNA (+) | Tomato plants | Colorimetric assay | 6 copies/μL | 30 | 65 | [27] |
Mayaro virus | ssRNA (+) | Cell culture | Fluorescence-based point-of-care device | 10 copies/reaction | 30 | 60 | [28] |
Japanese encephalitis virus (JEV) | ssRNA (+) | Cell culture | Colorimetric assay | 1 copy/μL | 30 | 60 | [29] |
Zika virus | ssRNA (+) | Tissue culture | Fluorescence Genie III | 6 copies/reaction | 30 | 65 | [30] |
Zika virus | ssRNA (+) | Cell culture | Colorimetric-based toehold switch sensor | 1.7 × 106 copies/mL | 30 | 37 | [31] |
HPV | Cervical swabs | Colorimetric-based microfluidic chip | 50 copies/reaction | 60 | 68 | [32] | |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal aspirates and sputum samples | Colorimetric DNAzyme reaction | 1 × 105 copies/mL | 30 | 65 | [33] |
SAR-CoV-2 virus | ssRNA (+) | Respiratory swab specimens | CRISPR-Cas12a-mediated fluorescence detection | 30 copies/μL | 40 | 60 | [34] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal swabs | High-fidelity DNA polymerase-mediated fluorescence detection | 115 copies/reaction | 30 | 60 | [35] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal and throat swabs | Cy5 channel fluorescence detection | 20 copies/reaction | 30 | 65 | [36] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal, throat, and nose swabs | Lab-on-chip platform-based fluorescence detection | 10 copies/reaction | 30 | 63 | [37] |
SAR-CoV-2 virus | ssRNA (+) | Pharyngeal swab specimen | Colorimetric assay | 30 copies/reaction | 60 | 65 | [38] |
SAR-CoV-2 virus | ssRNA (+) | Clinical throat swab | Colorimetric and fluorescence assay | 80 copies/mL | 30 | 65 | [39] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal swabs | Colorimetric and fluorescence assay | 50 copies/reaction | 31 | 65 | [40] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal and throat swabs | Colorimetric-based electromechanical device | 103 copies/mL | 30 | 65 | [41] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal swabs | Colorimetric assay | 0.75 copies/μL | 55 | 65 | [42] |
SAR-CoV-2 virus | ssRNA (+) | Saliva samples | Fluorescence detection | 5 copies/μL | 45 | 65 | [43] |
SAR-CoV-2 virus | ssRNA (+) | Wastewater samples | Colorimetric-based electrochemical sensor | 38 × 10−6 ng/μL | 30 | 60 | [44] |
Type of Virus | Target | Sample | Detection Methods | LOD | Time (min) | Temperature (°C) | Ref. |
---|---|---|---|---|---|---|---|
Rabies virus | ssRNA (−) | Cell culture | IX51 Olympus fluorescence detection | 100 copies/μL | 30 | 50 | [67] |
Influenza A (H1N1) virus | ssRNA (−) | Cell culture | CRISPR-Cas12a nuclease reaction | 10 copies/reaction | 20 | 37 | [68] |
Influenza A (H7N9) virus | ssRNA (−) | Cell culture | Fluorescence detection | 14 copies/μL | 10 | 42 | [61] |
Influenza A and B | ssRNA (−) | Nasal fluid samples | Fluorescence-based H-sandwich detection | 200 copies/mL | 20 | 37 | [66] |
African swine fever virus (ASFV) | Swine sample | Glycerol-enhanced one-pot CRISP-Cas12a nuclease reaction | 10 copies/μL | 60 | 37 | [69] | |
SAR-CoV-2 virus | ssRNA (+) | Respiratory swabs | CRISPR-Cas12a nuclease reaction | 50 copies/μL | 20 | 40 | [70] |
SAR-CoV-2 virus | ssRNA (+) | Respiratory swabs | Real-time fluorescence and dipstick detection | 130 copies/reaction | 30 | 39 | [71] |
SAR-CoV-2 virus | ssRNA (+) | Respiratory swabs | Cas12a nuclease reaction | 6 copies/μL | 30 | 37 | [72] |
SAR-CoV-2 virus | ssRNA (+) | Clinical throat swab | Lateral flow | 100 copies/reaction | 5 | 42 | [73] |
SAR-CoV-2 virus | ssRNA (+) | Clinical throat swab | CRISPR-Cas12a cleavage reaction and LED readout | 20 copies/μL | 20 | 37 | [64] |
Potato virus Y and S | ssRNA (+) | Cell culture | Nucleic acid lateral flow | 5 × 109 copies/reaction | 30 | 37 | [74] |
HIV-1 virus | ssRNA (+) | HIV-1 integrated cells | Fluorescence-based microfluidic device | 100 copies/mL | 30 | 37 | [75] |
HIV | ssRNA (+) | HIV clinical samples | CRISPR-mediated cascade reaction biosensor using a glucose meter | 43 copies/reaction | 60 | 40 | [76] |
Citrus tristeza virus | ssRNA (+) | Plant samples | Lateral flow immunochromatographic assay | 3.77 × 105 copies/mL | 20 | 40 | [74] |
Senecavirus A | ssRNA (+) | Piglet blood samples | Lateral flow dipstrip | 15 copies/μL | 25 | 35 | [77] |
Canine distemper virus | ssRNA (−) | Nasal/oropharyngeal swab | Real-time fluorescence detection | 9.4 copies/μL | 12 | 40 | [78] |
Chilli Veinal mottle virus | ssRNA (+) | Tobacco plant | Agarose gel electrophoresis | 10 fg/μL | 20 | 38 | [79] |
Wheat mosaic virus | ssRNA (+) | Wheat leaf | Agarose gel electrophoresis | 10−3 ng/μL | 20 | 45 | [80] |
Dengue virus | ssRNA (+) | Clinical specimens | Lateral flow dipstick | 10 copies/μL | 15 | 37 | [81] |
Type of Virus | Target | Sample | Detection Methods | LOD | Time (min) | Temperature (°C) | Ref. |
---|---|---|---|---|---|---|---|
Respiratory syncytial virus | ssRNA (−) | Nasopharyngeal aspirate | Real-time fluorescence detection | 35 copies/reaction | 30 | 39 | [16] |
Hepatitis D virus | ssRNA (+) | Plasma sample | Fluorescence and lateral flow strip | 10 copies/μL | 30 | 39 | [89] |
Coxsackievirus A10 and A6 | ssRNA (+) | Clinical sample | Real-time fluorescence detection | 35 copies/reaction | 30 | 39 | [85] |
Japanese encephalitis virus | ssRNA (+) | Aborted fetuses and testicular swollen boars | Real-time fluorescence detection | 5.5 copies/μL | 30 | 39 | [86] |
Human norovirus | ssRNA (+) | Stool clinical samples | Fluorescence-based microfluidic chip | 1.02 × 100 copies/μL | 20 | 39 | [90] |
SAR-CoV-2 virus | ssRNA (+) | Nasopharyngeal swabs | CRISPR-Cas13a electrochemical assay | 1.66 × 101 aM | 30 | 42 | [91] |
Platform | Manufacturer | Assay | Specimen | Analysis Time | LOD |
---|---|---|---|---|---|
CBDNA RT-LAMP RAPID TEST | Centrum Badan DNA, Poland | RT-LAMP | Nasopharyngeal swab | 20 | 10 copies/reaction |
CBDNA RT-LAMP RAPID TEST | DNA Research Center Ltd., Poland | RT-LAMP | Nasal swab, nasopharyngeal swab, saliva, and throat swab | 15 | 10 copies/reaction |
GenomtecSARS-CoV-2 EvaGreen® RT-LAMP CE-IVD Duo Kit | Genomtec SA, Poland | RT-LAMP | Nasopharyngeal swab, oropharyngeal swab, and saliva | 30 | 20 copies/reaction |
SARS-CoV-2 EvaGreen® Direct-RT-LAMP CE-IVD Kit | Genomtec SA, Poland | RT-LAMP | Nasopharyngeal swab, oropharyngeal swab, and saliva | 40 | 2 copies/reaction (saliva)10 copies/reaction (dry swab) |
GENEDIA W COVID-19 Colorimetric LAMP premix kit | Green Cross Medical Science Corp., South Korea | RT-LAMP | Nasopharyngeal swab and oropharyngeal swab | 32 | 100 copies/reaction |
Hayat Rapid Colorimetric & Fluorimetric One Step LAMP SARS-CoV-2 Test Kit | Hayat Genetics Inc., Turkey | RT-LAMP | Nasal swab, nasopharyngeal swab, and saliva | 30 | 5 copies/reaction |
COVID-19 Nucleic Acid Detection Kit (RT-LAMP) | Langfang Xinruikang Biotechnology Co. Ltd., China | RT-LAMP | Anterior nasal swab, nasopharyngeal swab, and oropharyngeal swab | 30 | 500 counts/min |
Vivid COVID-19 LAMP Direct-G | MultiplexDX s.r.o., Slovakia | RT-LAMP | Biological fluids, sputum, throat secretion | 40 | 1000 counts/min |
LAMPIGEN COVID19 RT-LAMP PCR KIT | Pharmaline AS, Turkey | RT-LAMP | Anterior nasal swab, nasal swab, nasopharyngeal swab, and throat swab | 30 | 3 copies/μL |
1copy™ COVID-19 MDx Kit Professional | 1drop Inc., South Korea | RT-LAMP | Nasopharyngeal swab | 20 | 100 copies/reaction |
Atila iAMP COVID-19 SANO Assay | Atila BioSystems Inc., United States | RT-LAMP | Nasopharyngeal swab, oropharyngeal swab, saliva | 70 | AU 2.5 |
BiologyWorks | BiologyWorks Inc., United States | LAMP | Anterior nasal swab, nasal swab | 45 | 30,000 counts/min |
C4Covid-19 Human | C4Diagnostics, France | RT-LAMP | Saliva | 30 | 210,000 AU |
DigiGENE™ COVID-19 Integrated Molecular Test | Canary Global Inc., Canada | RT-LAMP | Mid-turbinates swab, oropharyngeal swab | 20 | 600 counts/min |
SARS-CoV-2 Nucleic Acid Detection Kit | CapitalBio Technology, China | RT-LAMP | Nasal swab, nasopharyngeal swab, throat swab | 45 | 150 counts/min |
Dotz SARS-CoV-2 Rapid Diagnostic Kit | Dotz Nano Ltd., Israel | RT-LAMP | Nasopharyngeal swab, oropharyngeal swab, saliva | 34 | 1250 copies/reaction |
SARS-CoV-2 POC | Enbiotech s.r.l, Italy | RT-LAMP | Nasopharyngeal swab, oropharyngeal swab | 60 | 50 copies/reaction |
COV19-ID Kit | Genedrive, United Kingdom | RT-LAMP | Nasal swab | 17 | 500 counts/min |
LoopDeetect COVID 19 IC | LoopDeeScience, France | RT-LAMP | Anterior nasal swab, nasal swab, nasopharyngeal swab, oropharyngeal swab | 45 | - |
MD-Bio BCC19 Test Kit | MD-Bio Inc., United States | RT-LAMP | Nasal swab, nasopharyngeal swab | 30 | 75% |
NaorCov19 | Rapid Diagnostic Systems Limited, Israel | RT-LAMP | Saliva | 40 | 40 copies/μL |
Multitest COVID-19 | Selfdiagnostics Deutschland GmbH, Germany | RT-LAMP | Anterior nasal swab | 45 | - |
Dr Vida pocket for COVID-19 | STAB VIDA, Portugal | RT-LAMP | Nasopharyngeal swab | 40 | 75 particles |
Vicare Rapid FL | Vicare Solution GmbH, Germany | RT-LAMP | Deep (cough) sputum, nasal swab, nasopharyngeal swab, oropharyngeal swab, saliva, sputum | 30 | 150 cpu |
SARS-CoV-2 Isothermal Amplification Detection Kit | Xiamen Jiqing Biomedical Technology Co. Ltd., China | RT-LAMP | Nasal swab, throat swab | 30 | 500 counts/min |
ID NOWTM COVID-19 | Abbott | NEAR | nasopharyngeal swab | 15 | 125 counts/min |
Lucira COVID-10 All-In-One Test Kit | Lucira Health | RT-LAMP | Nasal swab | 30 | 900 counts/min |
POA-nCiVn-LFD-16 ket | BioPOA Co., Ltd. Korea | RPA | Nasopharyngeal swab and oropharyngeal swab | 20 | 20 copies/reaction |
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Ngoc, L.T.N.; Lee, Y.-C. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. Biosensors 2024, 14, 97. https://doi.org/10.3390/bios14020097
Ngoc LTN, Lee Y-C. Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms. Biosensors. 2024; 14(2):97. https://doi.org/10.3390/bios14020097
Chicago/Turabian StyleNgoc, Le Thi Nhu, and Young-Chul Lee. 2024. "Current Trends in RNA Virus Detection via Nucleic Acid Isothermal Amplification-Based Platforms" Biosensors 14, no. 2: 97. https://doi.org/10.3390/bios14020097