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VOLUME 1 , ISSUE 1 ( January-December, 2022 ) > List of Articles

REVIEW ARTICLE

Accurate LAMP-Enabled Rapid Test (ALERT) for COVID-19 detection: a need of the hour

Anita Sharma, Puran Parihar, Arvind Nanera, Sumeru Samanta, Neha Sharma, Sohil Takodara

Keywords : Loop Mediated Isothermal Amplification, Rapid Molecular diagnosis, Immunoassays, RTPCR, COVID- 19

Citation Information : Sharma A, Parihar P, Nanera A, Samanta S, Sharma N, Takodara S. Accurate LAMP-Enabled Rapid Test (ALERT) for COVID-19 detection: a need of the hour. 2022; 1 (1):2-14.

DOI: 10.5005/jamu-1-1-2

License: CC BY-NC 4.0

Published Online: 01-01-2022

Copyright Statement:  Copyright © 2021; The Author(s).


Abstract

Current situation of the COVID-19 pandemic, India has witnessed a massive surge of cases. As of April 30, 2021, around 400000 new cases and 3000-4000 deaths per day were reported from 32 states/union territories in India. In this national emergency health system is struggling and made every attempt for early and accurate diagnosis followed by isolation, treatment, and supportive care of COVID infected patients, to curtail the situation. Since the early days of the upsurge, researchers are working on the need for such assays. Currently, two major categories of diagnostic assays are available for diagnosing COVID-19. The first one is an immunoassay that identifies antigenic proteins or antibodies produced against these antigens, which is rapid but with low specificity and low sensitivity. The second option is sophisticated and complex molecular assays including RTPCR, microarray, next-generation sequencing (NGS), and crisper-based techniques that are confirmatory & highly sensitive, but their turnaround time is long and they require skilled and trained personals. Loop-mediated isothermal amplification (LAMP) is a molecular technique with all the benefits of molecular assay like accuracy & sensitivity, simultaneously it is rapid, reliable, costeffective, and could be used at point-of-care testing. This review discusses the procedure, clinical applications, advantages, and limitations of RT-LAMP in the context of immunoassay and RT-PCR technique. The review also focuses on recent advances and developments in LAMP-based techniques, its limitation, and challenges.

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  1. Ribiero de silva SJ, Alves De silva CT, Guarines KM, Mendes RP, Pardee K, Kohl A, et al. Clinical and Laboratory Diagnosis of SARS-Co V-2, the Virus Causing COVID-19. ACS Infect Dis. 2020;6(9): 2319-36.
  2. Augustine R, Hasan A, Das S, Ahmed R, Mori Y, Notomi T, et al. Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Corona viruses in the Context of COVID-19 Pandemic. Biology (Basel) 2020 Jul 22;9(8):182.
  3. Mori Y, Notomi T. Loop-mediated isothermal amplification (LAMP): Expansion of its practical applicationas a tool to achieve universal health coverage. J Infect Chemother. 2020; 26:13-17.
  4. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, et al. Loop-mediatedisothermal amplification of DNA. Nucleic Acids Res. 2000;28:63.
  5. Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification usingloop primers. Mol Cell Probes. 2002;16:223-9.
  6. Parida M, Horioke K, Ishida H, Dash PK, Saxena P, Jana AM, et al. Rapid detection and differentiation of dengue virus serotypes by a real-timereverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol. 2005;43:2895-2903.
  7. Parida MM, Santhosh SR, Dash PK, Tripathi NK, Lakshmi V, Mamidi N, et al. Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay. J Clin Microbiol. 2007;45:351-7.
  8. Chen HT, Zhang J, Ma YP, Ma LN, Ding YZ, Liu XT, et al. Reverse transcription loop-mediated isothermal amplification for the rapid detection of infectiousbronchitis virus in infected chicken tissues. Mol Cell Probes. 2010; 24:104-6
  9. Wong YP, Othman S, Lau YL, Radu S, Chee HY. Loop-mediated isothermal amplification (LAMP): A versatile technique for detection of micro-organisms. J. Appl Microbiol. 2018;124:626-643.
  10. Interim guidelines for collecting, handling, and testing clinical specimens for COVID-19: CDC; 2020 [updated 2020 Jul 8]. Available from: https://www.cdc.gov/coronavirus/2019-nCoV/lab/guidelines-clinical-specimens.html (Accessed on May 10, 2020).
  11. Wang W, Xu Y, Gao R. Detection of SARS-CoV-2 in different types of clinical specimens. JAMA. 2020; 323(18): 1843--4.
  12. Tomita N, Mori Y, Kanda H, Notomi T. Loopmediated isothermal amplification (LAMP) of genesequences and simple visual detection of products. Nat Protoc. 2008;3:877-882
  13. Saharan P, Khatri P, Dingolia S, Duhan JS, Gahlawat SK. Rapid detection of viruses using loopmediatedisothermal amplification (LAMP): A review in Biotechnology: Prospects and Applications; Springer: Delhi, India, 2013; Volume 9788132216, pp. 287-306. ISBN 9781461414094
  14. Torres C, Vitalis EA, Baker BR, Gardner SN, Torres, M.W, Dzenitis JM. LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures. BMC Bioinform. 2011;12:240
  15. Pooled Sample Testing and Screening Testing for COVID-19: FDA; 2020. Available from: https://www.fda.gov/medical-devices/coronaviruscovid-19-andmedical-devices/pooled-sample-testingand-screening-testing-covid-19 (Accessed on May 10, 2020).
  16. Paris DH, Imwong M, Faiz AM, Hasan M, Yunus EB, Silamut K, et al. Loop-mediated isothermal PCR (LAMP) for the diagnosis of falciparum malaria. Am J Trop Med Hyg. 2007;77:972-6.
  17. Tao ZY, Zhou HY, Xia H, Xu S, Zhu HW, Culleton RL, et al. Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium vivax infection. Parasites Vectors. 2011;4:115
  18. Miyamoto S, Sano S, Takahashi K, Jikihara T. Method for colorimetric detection of double-stranded nucleic acid using leucotriphenylmethane dyes. Anal Biochem. 2015;473: 28-33.
  19. Carter LJ, Garner LV, Smoot JW, Li Y, Zhou Q, Saveson CJ, et al. Assay Techniques and Test Development for COVID-19 Diagnosis. ACS Cent Sci. 2020 May 27;6(5):591-605.
  20. Serology-based tests for COVID-19 Johns Hopkins Center for Health Security. Available on www.center for health security.org/resources/COVID-19/serology/Serology-based-tests-for-COVID-19.html, (Accessed on May 14, 2020).
  21. Loeffelholz M J, Tang YW. Laboratory diagnosis of emerging human coronavirus infections - the state of the art. Emerging Microbes Infect. 2020; 9(1):747-756.
  22. FDA Fact Sheet: Serological testing for antibodies to SARSCoV-2 infection. U.S. Food & Drug Administration, Available on www.fda.gov/media/137111, Accessed on 14/05/2020.
  23. Minghua J, Weihua P, Amir A, Wenjie F, Liyan L, Hua F, et al Development and Validation of a Rapid, Single-Step Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) System Potentially to Be Used for Reliable and High Throughput Screening of COVID-19. Frontiers in Cellular and Infection Microbiology 2020; 10:331
  24. Nguyen T, Duong Bang D, Wolff A. 2019 Novel Coronavirus Disease (COVID-19): Paving the Road for Rapid Detection and Point-of-Care Diagnostics. Micromachines (Basel). 2020;11(3):306. P
  25. Andryukov BG, Natalya N. Besednova NN, Kuznetsova TA, Fedyanina LN. Laboratory-Based Resources for COVID-19 Diagnostics: Traditional Tools and Novel Technologies. A Perspective of Personalized Medicine. J Pers Med 2021; 11: 42
  26. Francois P, Tangomo M, Hibbs J, Bonetti E J, Boehme CC, Notomi T et al. Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. FEMS lmmunol Med Microbial. 2011; 62:41--48
  27. Galvez LC, Barbosa CFC, Koh RBL, Aquino VM. Loop-mediated isothermal amplification (LAMP) assays for the detection of abaca bunchy top virus and banana bunchy top virus in abaca. Crop Prot. 2020; 131: 105101.
  28. Wu D, Kang J, Li B, Sun D. Evaluation of the RTLAMP and LAMP methods for detection of Mycobacterium tuberculosis. J Clin Lab Anal. 2018 May;32(4):e22326.
  29. Lee MF, Chen YH, Peng CF. Evaluation of reverse transcription loop mediated isothermal amplification in conjunction with ELISA hybridization assay for molecular detection of Mycobacterium tuberculosis. J Microbial Methods. 2009;76: 174-180
  30. Lau SC, Liu WT. Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities. FEMS Microbial Lett. 2007;275:183-190.
  31. Parida MM. Rapid and real-time detection technologies for emerging viruses of biomedical importance. J Biosci. 2008;33:617-628.
  32. Biswas G, Sakai M. Loop-mediated isothermal amplification (LAMP) assays for detection and identification of aquaculture pathogens: Current state and perspectives. Appl Microbial Biotechnol. 2014;98:2881-2895.
  33. Hosaka N, Ndembi N, Ishizaki A, Kageyama S, Numazaki K, Ichimura H. Rapid detection of humanimmunodeficiency virus type 1 group M by a reverse transcription-loop-mediated isothermal amplificationassay. J Virol Methods. 2009; 157: 195-9.
  34. Toriniwa H, Kamiya T. Rapid detection and quantification of Japanese encephalitis virus by realtimereverse transcription loop-mediated isothermal amplification. Microbial Immunol. 2006;50:379-387.
  35. Hagiwara M, Sasaki H, Matsuo K, Honda M, Kawase M, Nakagawa H. Loop-mediated isothermal amplification method for detection of human papillomavirus type 6, 11, 16, and 18. J Med Virol. 2007;79: 605-615.
  36. Teoh BT, Sam SS, Tan KK, Johari J, Danlami MB, Hooi PS. et al. Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification. BMC Infect Dis. 2013;13:387.
  37. Parida M, Posadas G, Inoue S, Hasebe F, Morita K. Real-Time Reverse Transcription Loop-Mediated Isothermal Amplification for Rapid Detection of West Nile Virus. J Clin Microbiol. 2004;42: 257-263.
  38. Okafuji T, Yoshida N, Fujino M, Motegi Y, Ihara T, Ota Y, et al. Rapid diagnosticmethod for detection of mumps virus genome by loop-mediated isothermal amplification. J Clin Microbial. 2005;43:1625-1631.
  39. Imai M, Ninomiya A, Minekawa H, Notomi T, Ishizaki T, Van Tu P, et al. Rapid diagnosis of H5Nl avian influenza virus infection by newly developed influenza H5 hemagglutin in gene-specific loop-mediated isothermal amplification method. J Virol Methods. 2007;141: 173-180.
  40. Imai M, Ninomiya A, Minekawa H, Notomi T, Ishizaki T, Tashiro M, et al. Development of HS-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenzavirus infection. Vaccine 2006;24:6679-6682.
  41. Thai HTC, Le MQ, Vuong CD, 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: 1956-1961
  42. Bhadra S, Jiang YS, Kumar MR, Johnson RF, Hensley LE, Ellington AD. Real-time sequence-validated loopmediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV). PLoS ONE 2015;10: e0123126
  43. Parida MM, Santhosh SR, Dash PK, Tripathi NK, Lakshmi V, Mamidi N, et al. Rapid and real-time detection of Chikungunya virus by reverse transcription loop-mediated isothermal amplification assay. J Clin Microbial. 2007; 45:351-357
  44. Paris DH, Imwong M, Faiz AM, Hasan M, Yunus EB, et al. Loop-mediated isothermal PCR (LAMP) for the diagnosis of falciparum malaria. Am J Trop Med Hyg. 2007;77(5): 972--6.
  45. Wu X, Chen L, Guo T, Wu X, Cai H. Rapid diagnosis of cisplatin-sensitive and resistant cervical squamous cell carcinomas by reverse transcription loop-mediated isothermal amplification. Int J Clin Exp Pathol. 2018;11(2):882-887.
  46. G1tca K, Rawicz-Pruszynski K, Mielko J, Mlak R, S1tdlak K, Polkowski WP. Rapid Detection of Free Cancer Cells in Intraoperative Peritoneal Lavage Using One-Step Nucleic Acid Amplification (OSNA) in Gastric Cancer Patients. Cells. 2020; 9(10):2168.
  47. Walls AC, Park Y, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 2020;180:1-12.
  48. Hoffmann M, Kleine-Weber H, Schroeder S, Kriiger N, Herder T, Erichsen S, et al. SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor. Cell 2020; 181:10.
  49. Huang WE, Lim B, Hsu CC, et al. RT-LAMP for rapid diagnosis of coronavirus SARS-CoV-2. Microb Biotechnol. 2020;13(4):950-961.
  50. Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H. The Architecture of SARS Co V-2 Transcriptome. Cell. 2020;181:914-921
  51. Alanagreh L, Alzoughool F, Atoum M. The Human Coronavirus Disease COVID-19: Its Origin, Characteristics, and Insights into Potential Drugs and Its Mechanisms. Pathogens 2020;9:331.
  52. Lamb LE, Bartolone SN, Ward E, Chancellor MB. Rapid detection of novel coronavirus/Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by reverse transcription-loop-mediated isothermal amplification. PLoS One. 2020;15(6):e0234682.
  53. 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 Jul 1;66(7): 975-977
  54. Wang D. One-potdetection of COVID-19 with real time reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and visual RT-LAMP assay. BioRxiv(2020)
  55. Lu R, Wu X, Wan Z, Li Y, Zuo L, Qin J, et al Development of a Novel Reverse Transcription Loop Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2. Virol Sin. 2020 Jun; 35(3): 344-347.
  56. Schmid Burgk JL, Li D, Feldman D, Slabicki M, Borrajo J, Stecker J. et al LAMP-Seq: Population Scale COVID-19 Diagnostics Using a Compressed Barcode Space. BioRxiv(2020)
  57. Rabe BA, Cepko C, SARS-Co V-2 detection using an isothermal amplification reaction and a rapid, inexpensive protocol for sample inactivation and purification. MedRxiv(2020)
  58. El-Tholoth M, Bau HH, Song J. A Single and Two Stage, Closed Tube, Molecular Test for the 2019 Novel Coronavirus (COVID-19) at Home, Clinic, and Points of Entry. Chem Rxiv (2020)
  59. Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, et al. CRISPR-Casl2-based detection of SARS-CoV-2. Nat Biotechnol. 2020 Jul;38(7):870-874.
  60. Joung J, Ladha A, Saito M, Segel M, Bruneau R, Huang MW, et al. Point-of-care testing for COVID-19 using SHERLOCK diagnostics, MedRxiv (2020)
  61. Jeong JH, Kim KH, Jeong SH, Park JW, Lee SM, Seo YH. Comparison of sputum and nasopharyngeal swabs for detection of respiratory viruses. J Med Viral. 2014;86:2122-2127.
  62. Tahamtan A, Ardebili A. Real-time RT-PCR in COVID-19 detection: issues affecting the results. Exp Rev Mol Diagn. 2020;20:453--454
  63. Kim JY, Ko JH, Kim Y, et al. Viral Load Kinetics of SARS-CoV-2 Infection in First Two Patients in Korea. J Korean Med Sci. 2020;35(7):e86.
  64. Osorio NS, Correia-Neves M. Implication of SARSCo V-2 evolution in the sensitivity of RT-qPCR diagnostic assays. Lancet Infect Dis. 2021;21(2):166-167.
  65. GISAID. Global Initiative on Sharing All Influenza Data. GISAID 2020. Available at https://www.gisaid.org. (Accessed on June 2, 2020).
  66. Jia B, Li X, Liu W, Lu C, Lu X, Ma L, et al. Whole Genome Based LAMP Primer Design for a Set of Target Genomes. Front. Microbiol. 2019;10:2860
  67. Centers for Disease Control and Prevention. 2020. Corona virus disease 2019 (COVID-19). Interim laboratory biosafety guidelines for handling and processing specimens associated with coronavirus disease 2019 (COVID-19). Available at https://www.cdc.gov/coronavirus/2019-ncov/lab/labbiosafety-guidelines.html. (Accessed on 6 May 2020).
  68. U.S. Environmental Protection Agency. 2020. Pesticide registration. List N: disinfectants for use against SARS-CoV-2. Available at https://www.epa.gov/pesticide-registration/list-ndisinfectants-use-against-sars-cov-2. (Accessed on 6 May 2020).
  69. Mitchell SL, George KS, Rhoads DD, Susan M. Wu B, Dharmarha V. et al. Understanding, Verifying, and Implementing Emergency Use Authorization Molecular Diagnostics for the Detection of SARSCo V-2 RNA Journal of Clinical Microbiology. 2020; 58 (8):e00796-20
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