year 17, Issue 3 (May - June 2023)                   Iran J Med Microbiol 2023, 17(3): 294-300 | Back to browse issues page


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Ghiasi S M S, Yadollahi Movahed N, Esmaeili D. Rapid Detection of COVID-19 by RT-LAMP PCR Technique and its Comparison with Real-Time RT-PCR Method. Iran J Med Microbiol 2023; 17 (3) :294-300
URL: http://ijmm.ir/article-1-1811-en.html
1- Department of Cardiac Anesthesiology, Baqiyatallah University of Medical Sciences, Tehran, Iran
2- Department of Laboratory Science, Qom Branch, Islamic Azad University, Qom, Iran
3- Department of Microbiology and Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran , esm114@gmail.com
Abstract:   (1200 Views)

Background and Aim: Rapid antigen and antibody, serological tests, and RT ‑ PCR-based molecular methods are widely used to detect microorganisms worldwide. This study aimed to detect the covid-19 using Isothermal nucleic acid amplification techniques.
Materials and Methods: In this study, we collected 200 samples of nasopharynx and oropharynx from Jamaran Heart Hospital in Tehran. Covid -19 was examined by LAMP-RT PCR and Real-Time RT- PCR techniques. The nasopharynx and oropharynx nucleic acids were extracted both by pishtaz RNA extraction kit. LAMP-RT-PCR was performed on direct samples, while Real-Time RT-PCR samples were tested only using RNA extraction samples. The probe-primer mixture of this kit was designed using a dual-target gene method that simultaneously targets the genomic sequences of the spike region and N nucleocapsid. Fluorescence was measured using Real-Time RT-PCR and LAMP-RT PCR.
Results: Clinical specimens (56%) were positive using Real-Time RT-PCR technique, with mean Ct values less than 30. Clinical samples (52%) were positive for Covid-19 in the RT-LAMP technique of RNA extraction samples. RT-LAMP technique indicated a sensitivity of 92.8%. Also in the RT-LAMP method without RNA extraction, the sensitivity of the technique was 85.7%.
Conclusion: The LAMP-RT PCR technique is emerging as an appropriate alternative to the Real-Time RT-PCR method. This technique has basic advantages, such as constant temperature amplification, thermal cycle elimination, faster results, and potentially greater detection capacity. Therefore, the RT-LAMP-PCR can be used as a quick and cost-effective technique that can be employed in all areas.

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Type of Study: Original Research Article | Subject: Medical Bacteriology
Received: 2022/10/10 | Accepted: 2023/04/1 | ePublished: 2023/06/26

References
1. Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y, et al. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia. N Engl J Med. 2020;382(13):1199-207. [DOI:10.1056/NEJMoa2001316] [PMID] [PMCID]
2. Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020;382(8):727-33. [DOI:10.1056/NEJMoa2001017] [PMID] [PMCID]
3. Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-9. [DOI:10.1038/s41586-020-2008-3] [PMID] [PMCID]
4. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270-3. [DOI:10.1038/s41586-020-2012-7] [PMID] [PMCID]
5. World Health Organization. Coronavirus Disease (COVID-19) pandemic 2019. Available from: [https://www.who.int/emergencies/diseases/novel-coronavirus.]
6. World Health Organization. Coronavirus Disease (COVID-2019) situation 2019. Available from: [https://www.who.int/emergencies/diseases/novel-coronavirus.]
7. Shen M, Zhou Y, Ye J, Abdullah Al-maskri AA, Kang Y, Zeng S, et al. Recent advances and perspectives of nucleic acid detection for coronavirus. J Pharm Anal. 2020;10(2):97-101. [DOI:10.1016/j.jpha.2020.02.010] [PMID] [PMCID]
8. Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3):2000045. [DOI:10.2807/1560-7917.ES.2020.25.3.2000045] [PMID] [PMCID]
9. World Health Organization (WHO). Diagnostic testing for SARS-CoV-2 2020. Available from: [https://www.who.int/publications/i/item/diagnostic-testing-for-sars-cov-2.]
10. Damhorst GL, Duarte-Guevara C, Chen W, Ghonge T, Cunningham BT, Bashir R. Smartphone-Imaged HIV-1 Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) on a Chip from Whole Blood. Engineering. 2015;1(3):324-35. [DOI:10.15302/J-ENG-2015072] [PMID] [PMCID]
11. Abu Naser M, Jana H, Guido van M, Kanti P, Byron B, Thomas G, et al. Development and validation of direct RT-LAMP for SARS-CoV-2. MedRxiv. 2020(04).
12. Eftekhari A, Alipour M, Chodari L, Maleki Dizaj S, Ardalan M, Samiei M, et al. A comprehensive review of detection methods for SARS-CoV-2. Microorganisms. 2021;9(2):232. [DOI:10.3390/microorganisms9020232] [PMID] [PMCID]
13. Diao B, Wen K, Zhang J, Chen J, Han C, Chen Y, et al. Accuracy of a nucleocapsid protein antigen rapid test in the diagnosis of SARS-CoV-2 infection. Clin Microbiol Infect. 2021;27(2):289.e1-.e4. [DOI:10.1016/j.cmi.2020.09.057] [PMID] [PMCID]
14. World Health Organization. WHO Director-General's opening remarks at the media briefing on COVID-19 2020.
15. Oran E, Adi B-D, Hadar A, Virginia L, Areej K, Batya M, et al. Specific Detection of Sars-Cov-2 B.1.1.529 (Omicron) Variant By Four Rt-Qpcr Differential Assays. MedRxiv. 2021(2021):12.
16. World Health Organization (WHO). Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health 2021.
17. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):E63. [DOI:10.1093/nar/28.12.e63] [PMID] [PMCID]
18. Zhou Y, Wan Z, Yang S, Li Y, Li M, Wang B, et al. A mismatch-tolerant reverse transcription loop-mediated isothermal amplification method and its application on simultaneous detection of all four serotype of dengue viruses. Front Microbiol. 2019;10:1056. [DOI:10.3389/fmicb.2019.01056] [PMID] [PMCID]
19. Li Y, Zhou Y, Ma Y, Xu R, Jin X, Zhang C. A mismatch-tolerant RT-LAMP method for molecular diagnosis of highly variable viruses. Bio Protocol. 2019;9(21):e3415-e. [DOI:10.21769/BioProtoc.3415]
20. Thai Hong Thi C, Le Mai Q, Vuong Cuong D, Parida M, Minekawa H, Notomi T, et al. Development and Evaluation of a Novel Loop-Mediated Isothermal Amplification Method for Rapid Detection of Severe Acute Respiratory Syndrome Coronavirus. J Clin Microbiol. 2004;42(5):1956-61. [DOI:10.1128/JCM.42.5.1956-1961.2004] [PMID] [PMCID]
21. Lu R, Wu X, Wan Z, Li Y, Zuo L, Qin J, et al. Correction to: Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2. Virol Sin. 2020;35(4):499-. [DOI:10.1007/s12250-020-00223-4] [PMID] [PMCID]
22. Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LPM, Kirrmaier D, et al. A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Sci Transl Med. 2020;12(556):eabc7075. [DOI:10.1126/scitranslmed.abc7075] [PMID] [PMCID]
23. Yinhua Z, Nelson O, Jin X, Luo S, Raphael Ohuru N, Hongping W, et al. Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP. MedRxiv. 2020(02).
24. TaŞtan C, Yurtsever B, KarakuŞ G, KanÇaĞi DD, Demir S, Abanuz S, et al. SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients. Turk J Biol. 2020;44(7):192-202. [DOI:10.3906/biy-2004-113] [PMID] [PMCID]
25. Zheng J. SARS-CoV-2: un coronavirus emergente que causa una amenaza global [Internet]. Int J Biol Sci. 2020;16(10):1678-85. [DOI:10.7150/ijbs.45053] [PMID] [PMCID]
26. Taylor S, Landry CA, Paluszek MM, Fergus TA, McKay D, Asmundson GJG. COVID stress syndrome: Concept, structure, and correlates. Depress Anxiety. 2020;37(8):706-14. [DOI:10.1002/da.23071] [PMID] [PMCID]
27. Wang D. One-pot detection of COVID-19 with real-time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and visual RT-LAMP assay. Biorxiv. 2020:2020-04. [DOI:10.1101/2020.04.21.052530]
28. Yu L, Wu S, Hao X, Dong X, Mao L, Pelechano V, et al. Rapid Detection of COVID-19 Coronavirus Using a Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) Diagnostic Platform. Clin Chem. 2020;66(7):975-7. [DOI:10.1093/clinchem/hvaa102] [PMID] [PMCID]
29. Meskini M, Esmaeili D. The study of formulated Zoush ointment against wound infection and gene expression of virulence factors Pseudomonas aeruginosa. BMC Complement Altern Med. 2018;18(1):1-10. [DOI:10.1186/s12906-018-2251-4] [PMID] [PMCID]
30. Khodaparast M, Esmaeili D. Threats to Arrangements COVID-19. J Med Public Health. 2022;3(6):1047.

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