ABOUT LAMP

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The basics

What is a lamp?

LAMP stands for loop-mediated isothermal amplification reaction. It’s a mouthful, but what it means is just a biochemical reaction that multiplies DNA. The DNA amplification part is what LAMP and PCR have in common, but then the methods start to differ. The LAMP reaction proceeds in a special way that involves the formation of a “loop” on the molecular level. Once the loop is formed, amplification starts. The amplification is much, much faster than PCR and produces more DNA as well. For that reason, LAMP is sometimes described as an “explosive” amplification reaction.

How can that be useful for diagnosis?

The amplification of DNA is specific. It can only start when the reaction mix contains short pieces of DNA that match the DNA of the sample.  We can make the reaction specific to SARS-CoV-2 virus by using short pieces of DNA called “primers” that are designed to match the genetic information of the virus. Then, you have a reaction mix that starts the LAMP reaction when virus is present in the sample, but it can never start when virus is not present in the sample. This way you have a confirmation of wether or not a sample from a certain person contained the virus – a doctor can use this information to diagnose a person with covid-19.

What does the RT- part mean?

So far we’ve been talking about DNA. But you may know that SARS-CoV-2 is an RNA virus, that means it has RNA as it’s carrier of genetic information. This is true, but we can still work with as if it were DNA, if we perform another step. That step is where the RT part comes from – it’s called Reverse Transcription. Simply a conversion of RNA to DNA, which is catalysed by another component of the our reactions – the reverse transcriptase. RT-LAMP is thus able to detect RNA in the sample, and deliver a result based on the amplification of DNA.

How can you tell the result?

We’ve just established that RT-LAMP is a reaction that is capable of triggering the multiplication of DNA, when a specific RNA sequence is present in a sample. But how can we possibly tell if there if this has happened in a specific test tube? LAMP is such an explosive amplification reaction, that the amount of DNA created by it rapidly shifts the chemical balance of the reaction solution. We can use indicator dyes, that change their color based on the amount of certain chemical byproducts that are formed by the DNA amplification. A biochemical reaction so powerful, that you can see it’s result with the naked eye!

viral RNA
purple reaction mix
blue positive result
SARS-CoV-2 detected
viral RNA
purple reaction mix
purple negative result
SARS-CoV-2 not detected

Where our LAMPs are different

Our two types oF reactions

RT-LAMP

Assemble the master mix, add the inactivated sample, and incubate for 30 minutes at 63 degrees. Easy, fast, cheap.

RT-LAMP

Can be done in 40 minutes from sample to result. Minimal hands-on time. Confidently able to diagnose all samples with infectious levels of virus. Color change from purple to blue.

bead-LAMP

Purify the sample and concentrate the RNA with magnetic beads, then start the LAMP reaction. Superior sensitivity.

bead-LAMP

Can be done in 50 minutes from sample to result. Involves a 15 minute hands on bead-purification step to concentrate viral RNA. Identifies also samples with very low levels of virus. Color change from red to yellow.

bead-LAMP as a massive increase in sensitivity

With a simple, fast and relatively cheap step of concentrating the sample with the use of magnetic beads, we can fit several times the volume of sample into a reaction! This enables the LAMP reactions to “kick off” even with samples that have a very low viral load and would be otherwise undetectable with LAMP or antigen tests. With bead-LAMP, one can approach the sensitivity of the gold-standard PCR tests.

Different samples can be used

Some RT-LAMP reactions only work with extracted RNA as a sample input. Not ours. It was developed to be compatible with a wide variety of sample inputs, and without the need to do an RNA extraction on these samples. Our RT-LAMP protocols work with swabs in popular swab media and with saliva and gargle. Gargle self-sampling has the best balance of sensitivity, safety, ease of use and comfort. Samples are then inactivated to kill the virus and preserve the RNA for detection by a very short incubation at 95 °C for five minutes in the presence of an inactivation solution. It should be noted that new transfter media that inactivate samples instantly are usually incompatible with RT-LAMP since they contain aggresive chemicals inhibiting the reaction itself.

Color change is more robust

For result readout, our protocols rely on a visual detection of two different by-products of DNA amplification. For our RT-LAMP protocol, we use a drop in the free magnesium concentration, which is visualised with the help of hydroxynaphtol blue dye by a color change from purple to sky blue. For bead-LAMP, we can use the color change caused by the drop of the pH in the sample as a result of DNA amplification. Then, the reaction turns from red to yellow with the help a dye called phenol red. We can’t use this color change in normal RT-LAMP, because then the reactions would not be compatible with different sample inputs. We can use it for bead-LAMP though, because we perform the short step of purifying the RNA on magnetic beads, thereby getting rid of the sample which can mess up the pH.

High sensitivity and specifity

Our RT-LAMP reactions are optimised to not give false positives and to fetch the maximum sensitivity possible. For more information on the sensitivity and specifity, read our manuscript on bioRxiv.

Open access approach makes RT-LAMP resistant to supply issues

A perfect test is useless when it can’t be deployed on a massive scale. This is why we’ve kept easy access a key component in developing our LAMP assays. Our protocols are public and up to date on our website, and open access protocols have been developed to use the wild type, non patented enzymes BstLF and HIV-RT. This enables anyone around the world to produce them without needing to pay licensing fees or get permission from any company. Only this way can we prevent supply chain issues that have hampered mass testing from the onset of the pandemic. No more running out of one proprietary component – everything is public and available for anyone to synthesise.

Our two types oF protocols

We provide protocols for RT-LAMP and bead-LAMP reactions. You can chose if you want to order most of the reagents and enzymes from companies, or if you want to express and purify your own enzymes, or make your own buffers. Protocols for both of these approaches are available on this website.

COMMERCIAL PROTOCOLS

  • Use commercially available reagents
  • Lowest amount of effort to set up
  • Batch tested products
  • Higher price per reaction
  • Prone to supply chain issues

Open access protocols

  • Use expressed and purified enzymes
  • More effort to set up
  • Batch testing has to be performed
  • Very low price per reaction
  • Resistant to supply chain issues

Cheap

A test for the price of a coffee

For under one Euro for the crude reagent costs of RT-LAMP, the low cost enables massive and rapid testing in almost all parts of the world.

Visual

Visual color readout

A simple, visual color switch indicates the change in reaction chemistry caused by the presence of the target SARS-CoV-2 molecule in the reaction mix.

Simple

low-tech protocol

Skipping the step of RNA extraction, no need for a thermocycler, no need for fluorescent detection: RT-LAMP reactions run at a constant temperature of 63 degrees and can be carried out in incubators, thermoblocks or even water baths. 

Fast

From sample to result in under 40 minutes

Skipping the step of RNA extraction, no need for a thermocycler, no need for fluorescent detection: RT-LAMP reactions run at a constant temperature of 63 degrees and can be carried out in incubators, thermoblocks or even water baths. 

Open access

Technology for anyone to use

We set out to develop a test anyone can use. Our open access protocols utilize open-access enzymes that any molecular biology lab can produce at low cost, circumventing reliance on large companies and bringing down the price per test to incredibly small numbers. Buffer compositions are non-proprietary and public. 

Self sampling

Easy and comfortable sampling method

Gargling has shown to be an effective, comfortable self sampling method for SARS-CoV-2 testing. The use of this self-sampling method decreases the workload of medical personnel, is more comfortable and has proven to be reliable. 

Scalable

compatible with high-throughout and adaptable to your conditions

RT-LAMP can be done at home with just a few tubes and a pipette, or in a clinical, high-throughput laboratory with liquid handling robotics, ovens and automatic plate readers. Scalability is a key concern for any real-world impact, and this method can be easily automated and adapted in high-tech clinical praxis.

Flexible

Compatible with different sample types

It doesn’t matter if you have swabs in viral transport medium, universal transport medium or saline, gargle in HBSS, saline or water, RT-LAMP and especially beadLAMP are compatible with a wide variety of sample inputs.

Safe

Cross-contamination prevention system

LAMP technology, in and of itself, is very sensitive to contamination. We have implemented a known contamination prevention system into our reactions, based on dUTP and a thermolabile UDG enzyme. This assures that false positives are at a minimum and increases comfort of lab workers.

LAMP vs PCR vs antigen

We need diverse tools to fight a pandemic of this scale. We can not say that LAMP is the best test in all cases, and flattening the curve will most likely require a complex strategy utilising all of these major test types. You can find a concise comparison of these technologies, how they work and what they differ in.

PCR test readout

PCR

What it detects

Viral RNA

How it works

Amplification of DNA which is visualised on a real-time fluorescence measurement.

Where it's done

Diagnostic labs

Sensitivity

Very high

Cost

High

Sample type

Swab preferred, RNA extraction preferred

Time to result

2 – 4 hours

RT-LAMP color readout

LAMP

What it detects

Viral RNA

How it works

Amplification of DNA which is visualised by a color change in the reaction tubes.

Where it's done

Diagnostic labs, doctor’s offices, at home.

Sensitivity

Moderate to high

Cost

Low

Sample type

Gargle, swab, saliva, no RNA extraction

Time to result

30 – 45 minutes

Antigen test source: Medakit Ltf

Antigen test

What it detects

Viral surface proteins

How it works

Antibody binds to a protein on the surface of the virus and is visualised on a lateral flow strip.

Where it's done

Diagnostic labs, doctor’s offices, at home.

Sensitivity

Low to moderate

Cost

Low to moderate

Sample type

Swab

Time to result

5 – 30 minutes