Advancements in Testing Strategies for COVID-19
Abstract
:1. Introduction
2. Detection Techniques of SARS-CoV-2
2.1. High Throughput Sequencing
2.2. Imaging
2.3. Microarrays
2.4. Molecular Assay-Based Diagnosis
2.4.1. PCR-Based Methods
Isothermal Amplification
RT-Loop-Mediated Isothermal Amplification (LAMP)
One-Pot Enzyme-Free Isothermal Amplification
RNA Auto Cycling
2.5. CRISPR Based Detection
2.6. Limitations of Molecular Diagnosis
2.7. Signal Readout Methods
2.8. Serological Testing
2.8.1. Antigen-Based Detection
2.8.2. Antibody-Based Detection
2.9. Challenges in Immunoassay-Based Diagnostics
3. Biosensors
3.1. Biosensor for Genome Based Detection
3.2. Biosensors for Surface Protein of SARS-CoV-2
3.2.1. Lateral Flow Immunoassays
3.2.2. Lateral Flow Assays
3.2.3. Microfluidic-Based Immunosensor
3.2.4. FET-Based Biosensor
3.3. Biosensors for the Detection of Antibodies
3.4. Miscellaneous Biosensor Technologies
3.4.1. Multiplexed Paper-Based Colorimetric Sensor
3.4.2. Nanotechnology-Based Sensors
3.4.3. Aptamer-Based Detection
3.4.4. Artificial Intelligence-Based Sensors
3.4.5. Electrochemical Biosensors
3.4.6. Surface Plasmon Resonance-Based Biosensor
3.4.7. Localized Surface Plasmon Resonance
3.4.8. Biosensors Designed for Alternative Target of SARS-CoV-2
4. An Overview of the Commercially Available Kits
5. Impacts of Mutants on Diagnosis
6. Summary and Future Directions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Molecular Assay | RNA | Test Format | Turnaround Time (min.) | Target Analyte | Validated Samples |
NAT reagent kit (Open source) | 60–120 <13 [32] 40–50 [33] 83 [34] 8 h (188 samples) [35] | N-gene,E-gene, S-gene, ORF1ab, RdRp gene, ORF1a, | Nasopharyngeal swab, Unknown, Oropharyngeal swab Nasal swab Bronchoalveolar lavage | ||
Cartridge based
| 36 [36], 45 [37], 30 [38] | Orf1ab, N-gene, RdRp | Nasopharyngeal, Oropharyngeal, Nasal swabs | ||
Dipstick
| <40 [39] | Orf1ab, N-gene | Nasopharyngeal | ||
Immunoassay | Antibody(serological) | Cartridge-based processing | 15 [40] | IgG, Total Antibody, IgM | Serum, Plasma |
Chemiluminescence | 15 [41] 29, 80, 120, 48 [42] | IgG, IgM, Total Antibody, Nucleocapsid protein, Unknown | Serum, Unknown samples | ||
Rapid diagnostic
| 15–20 60–90 [43] 10 [44] | IgG,N-protein, Total antibody Unknown | Serum Plasma Unknown saliva | ||
Reagent Kit
| 20 [45] <90 [46] | IgG, Total antibody,IgA,N-protein, Unknown | Serum Nasopharyngeal Unknown | ||
Antigen | Cartridge-based process
immunoassay (CLIA) | 15 [47] | N-protein, S-protein (RBD) N-protein | Nasopharyngeal swab Saliva Nasal swab Unknown Oropharyngeal swab | |
Rapid diagnostic
| 15 [48] 20–30 [49,50] | N-protein S-protein (unknown type) S-protein RBD S-protein S1 S-protein S2 | Nasopharyngeal swabs Nasal swab Saliva Unknown Oropharyngeal swab Sputum | ||
Reagent kit | 15 [51] | N-protein S-protein S1 S-protein (unknown type) | Nasopharyngeal swab Unknown Serum Nasal swab Oropharyngeal swab |
Target | Biosensors | Principle | LOD/Detection Time/Cutoff Value/Sensitivity, Specificity | Drawbacks/Targets | References |
Genome Based Detection | Label-free electrochemical biosensor | DNA hybridization of electrodeposited AuNPs immobilized with single-stranded nucleotide | - | RNA extraction Sensitive sample handling | [130] |
Plasmonic biosensors (optical-LSPR) | Dual-functional plasmonic biosensor combining the plasmonic photothermal (PPT) effect and localized surface plasmon resonance (LSPR) sensing transduction | 0.22 pmol/L, 3 min | From multigene mixture | [131] | |
Naked-eye colorimetric | Thiol-modified antisense oligonucleotide is used to cap AuNPs, which change color upon finding the target N-gene | 0.18 ng/μL, 10 min | N-gene | [132] | |
Viral Particle Based Detection | Cell-based biosensor | Membrane-engineered mammalian cell containing antibody to bind with S-antigen | 1 fg/mL, 3 min | Not applicable for the detection of variants. | [133] |
Nanoplasmonic sensors | Optical measurement of the SARS-CoV-2 particle | 370 vp/mL, 15 min | Restricted for the S-antigen | [134] | |
Field effect-based transistor | Graphene-coated sheets with SARS-CoV-2 antibody | 2.42 × 102 copies/mL (in clinical samples) | s-antigen | [135] | |
G-druplex-based biosensors | Whole genome | [136] | |||
Molecularly imprinted polymers | Monoclonal-type, synthetic antibodies of SARS-CoV-2 | - | Only applied to the S-antigen | [137] | |
eCovSens | Potentiostat-based sensor fluorine doped tin oxide + AuNPs immobilized with monoclonal antibody | 90 fmol/L, 10–30 s | S-antigen | [138] | |
Electrochemical Biosensor | Functionalized TiO2 nanotube-based electrochemical | 0.7 nmol/L, 30 s | S-glycoprotein | [139] | |
Lateral flow immunoassay | ACE2 enzyme binding captured antibody | 1.86 × 105 copies/mL | Spike antigen | [140] | |
Antibody Based Detection | Lateral flow immunoassay | Lanthanide-doped Nanoparticles | 0.06666, 10 min | Anti-SARS-CoV-2-IgG | [141] |
Immunochromatographic | 15 min, 85.2% and 100% | IgG-IgM combined | [142] | ||
Immobilization on AuNPs | 15 min, 88.66% and 90.63% | IgG-IgM combined | [40] | ||
Plasmon-enhanced biosensor | Grating Coupled Fluorescent Plasmonic (GC-FP) based on ELISA from dried blood spot samples | 30 min 100% and 100% | Multiplexed (IgG, IgM, IgA) | [143] | |
Opto-microfluidic | A microfluidic device fabricated by the electrodeposition of Au-nanospikes linked with the optic probe to detect the target by using localized surface plasmon resonance | 0.5 pmol/L, 30 min | Antibodies against the spike protein | [144] |
Variants (Notations, Lineages) | Identification Date and Countries and Total No. of Countries | Sequences (GISAID) | Notable Mutations Occur at S-Protein Notable Mutations (S-Protein) | Effect on Antigenicity | |||
(Alpha) B.1.1.7(VOC-202012/01, 20/501Y.V1) | UK, 20 November 2020 | 168 | 1,133,025 | 23 | 8 | N501Y, [223] D614G [224], P681H [225] | N501Y effects on RBD [226] No effect on the serum neutralization [227] |
(Beta) B.1.351, 501Y.V2; 20C/501Y.V2 | South Africa, 20 December | 110 | 10,095,100 | 21 | 9 | K417N, E484K, N501Y, D614G, A701V | K417T possibility escaping some monoclonal antibodies [228,229] |
(Delta) B.1.617.2 | India | 141 | 10,095,100 | 12 | S:P681R S:L452R, | Yes, Increased [230,231] | |
(Eta) B.1.525 | Nigeria | 80 | 9719 | 10 | aa:S:E484K aa:S:Q677H aa:S:F888L | Yes, reduce serum neutralization against IgG [232]. | |
(Gamma) P.1, 501Y.V3, | Brazil and Japan, 20 December | 74 | 68,754 | 17 | 10 | aa:S:E484K aa:S:N501Y aa:S:K417T aa:S:D614G, aa:S:H655Y | aa:S:E484K escape mutation affects the nAbs [233]. |
A.23.1 E484K | Ugenda Brazil UK | 48 | 1126 | 16 | 4 | aa:S:F157L aa:S:V367F aa:S:Q613H aa:S:P681R | Yes [234] |
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Asghar, R.; Rasheed, M.; ul Hassan, J.; Rafique, M.; Khan, M.; Deng, Y. Advancements in Testing Strategies for COVID-19. Biosensors 2022, 12, 410. https://doi.org/10.3390/bios12060410
Asghar R, Rasheed M, ul Hassan J, Rafique M, Khan M, Deng Y. Advancements in Testing Strategies for COVID-19. Biosensors. 2022; 12(6):410. https://doi.org/10.3390/bios12060410
Chicago/Turabian StyleAsghar, Rabia, Madiha Rasheed, Jalees ul Hassan, Mohsin Rafique, Mashooq Khan, and Yulin Deng. 2022. "Advancements in Testing Strategies for COVID-19" Biosensors 12, no. 6: 410. https://doi.org/10.3390/bios12060410
APA StyleAsghar, R., Rasheed, M., ul Hassan, J., Rafique, M., Khan, M., & Deng, Y. (2022). Advancements in Testing Strategies for COVID-19. Biosensors, 12(6), 410. https://doi.org/10.3390/bios12060410