Antigen, PCR, LAMP: what's in a test?

During the early stages of the COVID-19 pandemic there was much discussion generated on the types of detection kits available. The two common methods often discussed by media were the antigen test (not to be confused with the antibody test, which is used to find out if a person indeed was infected with the virus at some point; after isolation for example) and the polymerase chain reaction (PCR) test. Though these two tests have been readily utilised and studied over decades, the sheer amount of information being thrown at people has led to some confusion over the diagnostic approaches. In general, both tests are designed to identify active COVID-19 infections with the antigen test targeting the virus’ surface proteins and the PCR test targeting the viral RNA. 

The antigen test uses buffers to extract SARS-CoV-2 antigens (surface proteins) from the swab sample which are thenadded to a paper strip containing antibodies that have been designed to bind (grab on) to the antigens. The result is visualised as a band on the paper strip, similar to a pregnancy test, where if enough binding occurs a band of colour will appear on the paper. Overall, the antigen test has a shorter turnaround time and is cheaper than the PCR test, but this comes with the price of lower sensitivity. In the case of a low viral count, there may not be enough surface antigens available for the necessary amount of antibody binding to occur for a visibly positive result.

The PCR test, on the other hand, is able to accurately detect COVID-19 in low viral count samples by generating replicates of the target RNA. The way PCR achieves this feat is by utilising specific catalytic proteins (enzymes) called DNA polymerase. These enzymes (with the help of disease specific primers and temperature cycling) will seek out and convert the RNA into DNA then copy it millions of times which increases the flourescent signal that can be tracked in real time sensors. This is a massive advantage for PCR-based detection because as one can imagine, it is difficult to seek out and identify a handful of viral proteins or RNA particles when there are millions of non-viral contaminants also present in the patient sample. The equivalent is like finding a needle in a haystack! However, if you can increase the number of viral markers then the search becomes easier. This approach allows for both early detection of the disease and more accurate detection of asymptomatic patients. Considering these factors, there is no question as to why PCR is used more frequently between these two techniques. Unfortunately, the cost being paid for the high sensitivity is in fact the high price associated with running PCR. Both the reagent kits required to isolate the viral RNA away from contaminants that would inhibit the amplification reaction and the equipment used to meet the cyclic temperature demands of PCR are very costly. 

So where does Loop-Mediated Isothermal Amplification (LAMP) fit into the picture? LAMP is similar to PCR, in that it is a technique that replicates DNA but does so at a single temperature or isothermally. This means it has the same high sensitivity like PCR, making it useful for early infection and asymptomatic screening. However, unlike PCR, LAMP is much more affordable since the single temperature reaction does NOT require expensive temperature cyclers and it uses a more robust enzyme that is still functional in the presence of contaminants that would normally be harmful to PCR (i.e. there is no need for expensive RNA extraction kits). This means that a successful implementation of a LAMP-based diagnostic kit would be the best of both worlds; high sensitivity but at a fraction of the cost. Not to mention that it is even quicker!