A Precise Review on NAATs-based Diagnostic Assays for COVID-19: A Motion in Fast POC Molecular Tests

Overview

Journal Eur J Clin Invest

Publisher Wiley

Specialty General Medicine

Date 2022 Aug 22

PMID 35989561

Authors

Bahareh Maleki

Zohreh Hojati

Affiliations

Soon will be listed here.

Abstract

Background: Diagnosis is one of the main strategies to deal with infectious and deadly diseases such as coronavirus disease 2019 (COVID-19). The global pandemic of COVID-19 has led to an immediate need to expand rapid diagnostic techniques. New isothermal-based methods are being developed for COVID-19 detection aiming to resolve the limitations related to the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method through immediate samples processing and minimizing false-negative or ambiguous results. Advances in nucleic acid amplification techniques (NAATs) can provide affordable and easy-to-use diagnostic platforms with high sensitivity and specificity in order to be available to the public as approved commercial kits.

Aims: The development of point-of-care (POC) testing can assist in rapid clinical decision-making and mitigate burdens on health care facilities. Finally, we discussed the different diagnostic methods based on NAATs for COVID-19 in detail. Comparative parameters are addressed for all assays and Emergency Use Authorizations (EUA)-approved commercial tests are cited.

Conclusions: Isothermal-coupled methods and LAMP-based molecular methods have been suggested as suitable portable tests with high diagnostic speed for use in POC testing.

Citing Articles

Reusable Biosensor for Easy RNA Detection from Unfiltered Saliva.

Wityk P, Terebieniec A, Nowak R, Lubinski J, Mroczynska-Szelag M, Wityk T Sensors (Basel). 2025; 25(2).

PMID: 39860729 PMC: 11769206. DOI: 10.3390/s25020360.

A duplex HiFi-LAMP assay for screening of two novel human circoviruses HCirV-1 and HCirV-2.

Xu A, Zhang M, Chen X, Wan Z, Zhao Y, Wang J BMC Infect Dis. 2024; 24(1):1388.

PMID: 39639190 PMC: 11619094. DOI: 10.1186/s12879-024-10283-6.

Development of a rapid LFA test based on direct RT-LAMP for diagnosis of SARS-CoV-2.

Sadeghi N, Shirazi N, Dehbashi M, Maleki B, Cho W, Hojati Z Pract Lab Med. 2024; 42:e00437.

PMID: 39553462 PMC: 11565418. DOI: 10.1016/j.plabm.2024.e00437.

A systematic literature review on public health and healthcare resources for pandemic preparedness planning.

Beishuizen B, Stein M, Buis J, Tostmann A, Green C, Duggan J BMC Public Health. 2024; 24(1):3114.

PMID: 39529010 PMC: 11552315. DOI: 10.1186/s12889-024-20629-z.

A one-step low-cost molecular test for SARS-CoV-2 detection suitable for community testing using minimally processed saliva.

da Silva S, Amaral C, Malta-Luis C, Grilo D, Duarte A, Morais I Biol Methods Protoc. 2024; 9(1):bpae035.

PMID: 38835855 PMC: 11147803. DOI: 10.1093/biomethods/bpae035.

References

Compton J . Nucleic acid sequence-based amplification. Nature. 1991; 350(6313):91-2. DOI: 10.1038/350091a0. View

Smith E, Zhen W, Manji R, Schron D, Duong S, Berry G . Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection. J Clin Microbiol. 2020; 58(9). PMC: 7448672. DOI: 10.1128/JCM.01134-20. View

Leelawong M, Mitchell S, Fowler R, Gonzalez E, Hughes S, Griffith M . SARS-CoV-2 N gene mutations impact detection by clinical molecular diagnostics: reports in two cities in the United States. Diagn Microbiol Infect Dis. 2021; 101(3):115468. PMC: 8255188. DOI: 10.1016/j.diagmicrobio.2021.115468. View

Tian A, Elsheikha H, Zhou D, Wu Y, Chen M, Wang M . A novel recombinase polymerase amplification (RPA) assay for the rapid isothermal detection of Neospora caninum in aborted bovine fetuses. Vet Parasitol. 2018; 258:24-29. DOI: 10.1016/j.vetpar.2018.06.004. View

Deiman B, Van Aarle P, Sillekens P . Characteristics and applications of nucleic acid sequence-based amplification (NASBA). Mol Biotechnol. 2002; 20(2):163-79. DOI: 10.1385/MB:20:2:163. View

Iranzo J, Lobkovsky A, Wolf Y, Koonin E . Evolutionary dynamics of the prokaryotic adaptive immunity system CRISPR-Cas in an explicit ecological context. J Bacteriol. 2013; 195(17):3834-44. PMC: 3754601. DOI: 10.1128/JB.00412-13. View

Zhang W, Pan J, Li F, Zhu M, Xu M, Zhu H . Reverse Transcription Recombinase Polymerase Amplification Coupled with CRISPR-Cas12a for Facile and Highly Sensitive Colorimetric SARS-CoV-2 Detection. Anal Chem. 2021; 93(8):4126-4133. DOI: 10.1021/acs.analchem.1c00013. View

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H . Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020; 395(10224):565-574. PMC: 7159086. DOI: 10.1016/S0140-6736(20)30251-8. View

Demidov V . Rolling-circle amplification in DNA diagnostics: the power of simplicity. Expert Rev Mol Diagn. 2002; 2(6):542-8. DOI: 10.1586/14737159.2.6.542. View

10.

Ahmad S, Ali N, Kausar M, Misbah H, Wahid A . Road toward rapid-molecular point of care test to detect novel SARS-coronavirus 2019 (COVID-19): Review from updated literature. Allergol Immunopathol (Madr). 2020; 48(5):518-520. PMC: 7328543. DOI: 10.1016/j.aller.2020.06.001. View

11.

Li S, Cheng Q, Liu J, Nie X, Zhao G, Wang J . CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA. Cell Res. 2018; 28(4):491-493. PMC: 5939048. DOI: 10.1038/s41422-018-0022-x. View

12.

Guo L, Sun X, Wang X, Liang C, Jiang H, Gao Q . SARS-CoV-2 detection with CRISPR diagnostics. Cell Discov. 2020; 6:34. PMC: 7235268. DOI: 10.1038/s41421-020-0174-y. View

13.

Mitchell S, Ventura S . Evaluation and Comparison of the Hologic Aptima SARS-CoV-2 Assay and the CDC 2019-nCoV Real-Time Reverse Transcription-PCR Diagnostic Panel Using a Four-Sample Pooling Approach. J Clin Microbiol. 2020; 58(12). PMC: 7685873. DOI: 10.1128/JCM.02241-20. View

14.

Li S, Cheng Q, Wang J, Li X, Zhang Z, Gao S . CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 2018; 4:20. PMC: 5913299. DOI: 10.1038/s41421-018-0028-z. View

15.

El Jaddaoui I, Allali M, Raoui S, Sehli S, Habib N, Chaouni B . A review on current diagnostic techniques for COVID-19. Expert Rev Mol Diagn. 2021; 21(2):141-160. DOI: 10.1080/14737159.2021.1886927. View

16.

Hofmann W, Dries V, Herrmann E, Gartner B, Zeuzem S, Sarrazin C . Comparison of transcription mediated amplification (TMA) and reverse transcription polymerase chain reaction (RT-PCR) for detection of hepatitis C virus RNA in liver tissue. J Clin Virol. 2005; 32(4):289-93. DOI: 10.1016/j.jcv.2004.08.011. View

17.

Ding X, Yin K, Li Z, Lalla R, Ballesteros E, Sfeir M . Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun. 2020; 11(1):4711. PMC: 7501862. DOI: 10.1038/s41467-020-18575-6. View

18.

Dao Thi V, Herbst K, Boerner K, Meurer M, Kremer L, Kirrmaier D . A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci Transl Med. 2020; 12(556). PMC: 7574920. DOI: 10.1126/scitranslmed.abc7075. View

19.

Thompson D, Lei Y . Mini review: Recent progress in RT-LAMP enabled COVID-19 detection. Sens Actuators Rep. 2022; 2(1):100017. PMC: 7428436. DOI: 10.1016/j.snr.2020.100017. View

20.

Chaibun T, Puenpa J, Ngamdee T, Boonapatcharoen N, Athamanolap P, OMullane A . Rapid electrochemical detection of coronavirus SARS-CoV-2. Nat Commun. 2021; 12(1):802. PMC: 7864991. DOI: 10.1038/s41467-021-21121-7. View