Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations
Abstract
:1. Introduction
2. Nucleic Acid Amplification Technologies
2.1. Polymerase Chain Reaction (PCR) Methods
2.1.1. Fluorescence-Based Real-Time Quantitative PCR (qPCR)
2.1.2. Digital PCR (dPCR)
2.1.3. Multiplex PCR (mPCR)
2.2. Loop-Mediated Isothermal Amplification (LAMP)
3. Immunological Detection Methods
3.1. Colloidal Gold Immunochromatographic Assay (GICA)
3.2. Enzyme-Linked Immunosorbent Assay (ELISA)
3.3. Chemiluminescence Immunoassay (CMIA)
3.4. Fluorescence Labeled Immunochromatographic Assay (FICA)
4. Nucleic Acid Sequencing Methods
4.1. Clinical Metagenomic Next-Generation Sequencing (mNGS)
4.2. Nanopore Third-Generation Sequencing (NTS)
5. CRISPR-Based Detection Methods for SARS-CoV-2 Infection
6. Direct Isolation of SARS-CoV-2 from Clinical Samples of COVID-19 Patients
7. Concluding Remarks
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Ab | total antibodies |
ACE2 | angiotensin-converting enzyme 2 |
AIOD-CRISPR | all-in-one dual CRISPR–Cas12a |
BALF | bronchoalveolar lavage |
β-CoV | betacoronavirus |
bat-SL-CoVZC45 | bat SARS-like coronavirus |
CDC | Center for Disease Control |
CMIA | chemiluminescent immunoassay |
COVID-19 | coronavirus disease 2019 |
CRISPR | clustered regularly interspaced short palindromic repeats |
Ct | Relative threshold |
CT | computed tomography |
ddPCR | droplet digital PCR |
DETECTR | DNA endonuclease-targeted CRISPR trans reporter |
dPCR | digital polymerase chain reaction |
E | envelope protein |
ELISA | enzyme-linked immunosorbent assay |
FDA | Food and Drug Administration |
FICAs | fluorescence labeled immunochromatographic assays |
GICA | colloidal gold immunochromatographic assay |
HAS | human serum albumin |
HCV | hepatitis C virus |
HIV | human immunodeficiency virus |
IgG | immunoglobulin G |
IgM | immunoglobulin M |
LAMP | loop-mediated isothermal amplification |
LoD | limit of detection |
M | matrix protein |
MERS-CoV | Middle East respiratory syndrome coronavirus |
MHV | murine coronavirus |
mNGS | clinical metagenomic next-generation sequencing |
mPCR | multiplex PCR |
N | nucleocapsid protein |
NP | nasopharyngeal |
NPV | negative predictive value |
nsp | nonstructural protein |
NTS | nanopore sequencing (NTS) |
ONT | Oxford Nanopore Technologies |
PCR | polymerase chain reaction |
RdRP | RNA-dependent RNA polymerase |
RPA | recombinase polymerase amplification |
RTFQ-PCR | real-time fluorescent quantitative PCR |
S | surface glycoprotein |
SARS-CoV | severe acute respiratory syndrome virus |
SARS-CoV-2 | severe acute respiratory syndrome coronavirus 2 |
SHERLOCK | specific high-sensitivity enzymatic reporter unlocking |
TMPRSS2 | transmembrane serine protease 2 |
WGS | wide-genome sequencing |
WHO | World Health Organization |
ZIKV | Zika virus |
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Technique | Advantages | Disadvantages | References |
---|---|---|---|
Nucleic Acid Amplification Techniques | |||
RT-qPCR | High sensitivity and accuracy, absolute and relative quantification, low risk of contamination | Risk of false-positive or negative detection, primers, and reaction efficiency can affect testing outcome | [14,21,22] |
dPCR | High sensitivity and accuracy, absolute detection | Expensive | [34,35,38,40,41] |
Multiplex PCR | High sensitivity and accuracy, ability to detect multiple targets, cost-effective, simple workflow | Further optimization required for primer and reaction conditions, potential for contamination, potential for reaction failure | [43,54,55,59,60] |
LAMP | High sensitivity, thermal cycler not required, extensive sample processing not needed, quick, cost-effective | Sensitivity depends on sample complexity, difficult to prepare appropriate primer designs, lacks clinical data | [62,64,65,69] |
Immunological Detection Methods | |||
GICA | Simple workflow, rapid analysis, cost-effective | Cannot detect acute infections, low sensitivity and specificity | [74,79] |
ELISA | Simple workflow, rapid detection, no viral exposure | Cannot detect acute infections, low sensitivity | [86] |
CMIA | High sensitivity, automated application, rapid analysis | Expensive, results may not be accurate in the context of pre-existing immune dysfunction | [90,91] |
FICA | High sensitivity, can detect early infection, rapid analysis | Fluorescence quenching | [93,94,96,97] |
Nucleic Acid Sequencing Methods | |||
mNGS | Can detect any part of the genome, unbiased | Complicated and lengthy process, prone to contamination, expensive | [98,105] |
NTS | High sensitivity, can detect viral mutations, quick sample processing | Lengthy process, unable to detect RNA fragments < 200 bp, expensive | [107,112,113,114,115] |
CRISPR-Based Detection Methods | |||
CRISPR | Ultrasensitive, high specificity, rapid analysis | Multistep process is prone to contamination | [118,119,120] |
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Qasem, A.; Shaw, A.M.; Elkamel, E.; Naser, S.A. Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Curr. Issues Mol. Biol. 2021, 43, 728-748. https://doi.org/10.3390/cimb43020053
Qasem A, Shaw AM, Elkamel E, Naser SA. Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Current Issues in Molecular Biology. 2021; 43(2):728-748. https://doi.org/10.3390/cimb43020053
Chicago/Turabian StyleQasem, Ahmad, Ameera M. Shaw, Erij Elkamel, and Saleh A. Naser. 2021. "Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations" Current Issues in Molecular Biology 43, no. 2: 728-748. https://doi.org/10.3390/cimb43020053
APA StyleQasem, A., Shaw, A. M., Elkamel, E., & Naser, S. A. (2021). Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Current Issues in Molecular Biology, 43(2), 728-748. https://doi.org/10.3390/cimb43020053