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Biology

Published: September 8, 2023 doi: 10.3791/65662

Materials

Name Company Catalog Number Comments
1 kb DNA Ladder SOLIS BIODYNE 07-12-00050 Store at -20 °C
50x TAE Electrophoresis Buffer ThermoScientific B49 Store at roome temperature
Accuris High Fidelity Polymerase ACCURIS LIFE SCIENCE REAGENTS PR1000-HF-200 It can be used in case Q5 High-Fidelity DNA polymerase cannot be purchased. For the enzyme, make aliquots of an appropriate volume and store at -20 °C until use.
Agarose PanReacAppliChem A8963,0100 N/A
Bst 3.0 DNA Polymerase 8000 IU/mL New England BioLabs M0374S/M0374L For the enzyme, make aliquots of an appropriate volume and store at -20 °C until use.
Deoxynucleotide (dNTP) Solution Set New England BioLabs N0446S Store at -20 °C
Diethyl pyrocarbonate Sigma-Aldrich 159220-25G  Handle it with caution under an extraction cabinet
GeneRuler 100 bp Plus DNA Ladder, ready-to-use ThermoScientific SM0322 Store at -20 °C
Hydroxy naphthol blue disodium salt Santa Cruz Biotechnology sc-215156B N/A
Q5 High-Fidelity DNA polymerase 2000 IU/mL  New England BioLabs M0491S/M0491L For the enzyme, make aliquots of an appropriate volume and store at -20 °C until use.
WarmStart RTx Reverse Transcriptase 15000 IU/mL New England BioLabs M0380S/M0380L For the enzyme, make aliquots of an appropriate volume and store at -20 °C until use.

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References

  1. World Health Organization. Who coronavirus (COVID-19) dashboard (no date). , https://covid19.who.int/ (2023).
  2. Ibrahim, N. K. Epidemiologic surveillance for controlling Covid-19 pandemic: types, challenges and implications. Journal of Infection and Public Health. 13 (11), 1630-1638 (2020).
  3. Rojas-Gallardo, D. M., et al. COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance. (Molecular epidemiology of COVID-19 in Latin America). medRxiv. , (2020).
  4. Liu, R., et al. Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan, China, from Jan to Feb 2020. Clinica Chimica Acta. 505, 172-175 (2020).
  5. Kevadiya, B. D., et al. Diagnostics for SARS-CoV-2 infections. Nature Materials. 20 (5), 593-605 (2021).
  6. Tomita, N., Mori, Y., Kanda, H., Notomi, T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nature Protocols. 3 (5), 877-882 (2008).
  7. Li, Y., Fan, P., Zhou, S., Zhang, L. Loop-mediated isothermal amplification (LAMP): A novel rapid detection platform for pathogens. Microbial Pathogenesis. 107, 54-61 (2017).
  8. Notomi, T., Mori, Y., Tomita, N., Kanda, H. Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects. Journal of Microbiology. 53 (1), 1-5 (2015).
  9. Augustine, R., et al. Loop-mediated isothermal amplification (LAMP): A rapid, sensitive, specific, and cost-effective point-of-care test for coronaviruses in the context of COVID-19 pandemic. Biology (Basel). 9 (8), 182 (2020).
  10. Nextstrain. , https://nextstrain.org/ (2023).
  11. Biolabs, N.E. Neb Lamp, NEB LAMP. , https://lamp.neb.com/ (2023).
  12. PrimerDimer. , http://www.primer-dimer.com/ (2023).
  13. National Center for Biotechnology Information. Blast: Basic local alignment search tool (no date). , https://blast.ncbi.nlm.nih.gov/ (2023).
  14. Zhang, Y., et al. Rapid molecular detection of SARS-CoV-2 (COVID-19) virus RNA using colorimetric LAMP. medRxiv. , (2020).
  15. Lu, R., et al. Development of a novel reverse transcription loop-mediated isothermal amplification method for rapid detection of SARS-CoV-2. Virologica Sinica. 35 (3), 344-347 (2020).
  16. Najafov, A., Hoxhaj, G. PCR Guru. , Elsevier, Academic Press. (2017).
  17. Zhang, Y., et al. Enhancing colorimetric loop-mediated isothermal amplification speed and sensitivity with guanidine chloride. Biotechniques. 69 (3), 178-185 (2020).
  18. Ramírez-Chavarría, R. G., et al. Automatic analysis of isothermal amplification via impedance time-constant-domain spectroscopy: A SARS-CoV-2 case study. Chemosensors. 11 (4), 230 (2023).
  19. Haque, M. F. U., et al. A novel RdRp-based colorimetric RT-LAMP assay for rapid and sensitive detection of SARS-CoV-2 in clinical and sewage samples from Pakistan. Virus Research. 302, 198484 (2021).
  20. Donia, A., et al. Integration of RT-LAMP and microfluidic technology for detection of SARS-CoV-2 in wastewater as an advanced point-of-care platform. Food and Environmental Virology. 14, 364-373 (2022).
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Cite this Article

David-Jimenez, S. A., Caicedo, P.More

David-Jimenez, S. A., Caicedo, P. A., Villegas-Torres, M. F., Campillo-Pedroza, N. Detecting SARS-CoV-2 Virus by Reverse Transcription-Loop-Mediated Isothermal Amplification. J. Vis. Exp. (199), e65662, doi:10.3791/65662 (2023).

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