RT-LAMP based diagnostics

Method Overview:

The topic of this page is go describe a novel variant COVID-19 diagnostic method. In this page we describe the key features of this method and we also compare to the standard method RT-PCR. There is more methods that exist RT-LAMP is not the only method out there.

LAMP Introduction

Key features of LAMP:

Isothermal
Amplification is rapid
High strand displacement activity via polymerases
Uses 4-6 primes that recognizes 6-8 distinct regions of target nucleic acid
Thermal denaturation of dsDNA is not required
Cost effective
Time efficient
Colorimetric or fluorescent

RT-LAMP steps video

Figure 1 : This video shows step by step the procedure of RT-LAMP providing a clear and easy guideline.

RT-LAMP Diagram

Figure 2.

The figure show a interpretation the video. Made by Chris.

Amplification continues after Step 6 as long as it is heated. Amplification is exponential like PCR. More product = more intense output signal.

RT-PCR vs. RT-LAMP

RT-PCR

Temperature cycles up and down - needs lab equipment
Needs 2 primers (forward primer and reverse primer)
Takes long (45 minutes to 1 hour)
Product yield is lower
Visual detection not possible
Easier to multiplex

RT-LAMP

Isothermal - does not necessarily use lab equipment
Requires 4-6 primers (forward inner primer, forward outer primer, backwards inner primer, and backwards outer primer)
Faster (15-60 minutes but typically <30 mins)
Product yield is high
Visual detection possible
Difficult to multiplex

Keywords

RT-LAMP

Reverse Transcriptase Loop-Mediated Isothermal Amplification

(3)

Primer Design

Primers are short Nucleic Acid sequences that show the starting and ending point of the strand of DNA or RNA. Here is a link to a website which goes over the ways to design primers for RT-LAMP.

(4)

PrimerExplorer v5

Note: PrimerExplorer is for designing RT-LAMP Primers specifically.

Isothermal

Isothermal just means the assay stays at a constant temperature.

(5)

Relevant Papers

Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges

The paper overviews COVID-19, its etiology, and several nucleic acid amplification (NAA) test methods for diagnosing COVID. They went over 11 different methods in detail with how specific and sensitive each method was as well as in terms of other details - assay time, its operating temperature. The paper is relevant because it overviews several different NAA methods within a relatively short length without sacrificing on accuracy or detail. The paper is relevant to my chosen method topic because it explains what LOOP is, what it needs, and other related details on it - with a figure accompanying it.

(6)

Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

This paper focuses on using RT-LAMP test method to detect genomic RNA. This method according to the paper is easier to use and it is a lot easier to see a visible confirmation on whether or whether not the person has the virus. Also the method of visible conformation is colorimetric. This paper is a real world use of this method and even further a connection between RT-LAMP and SARS-CoV-2 detection.

(7)

References

(1) https://www.youtube.com/watch?v=L5zi2P4lggw.

(2) This is Chris' personal figure.

(3) Image found on Wikimedia Commons

(4) Image found from Pixabay

(5) Image found on Clipart Library

(6) Kilic, T., Weissleder, R., and Lee, H. (2020). Molecular and Immunological Diagnostic Tests of COVID-19: Current Status and Challenges. IScience 23.

(7) Park, G., Ku, K., Baek, S., Kim, S., Kim, B., and Maegni, J., (2020). Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The Journal of Molecular Diagnostic Vol 22.

Page updated

Report abuse