Comparing PCR to RT-LAMP for RNA Detection and The Importance for Hop Latent Viroid

Professor DeBacco

PCR- Polymerase Chain Reaction
Has primers that are specific to a nucleic acid region and if present and a positive binding occurs it will be copied multiple times, exponentially producing the original sequence
This can not only determine if the sequence is present or not, but with other detective instrumentation the severity (how many particles were present at the start).
Low or high viral (or viroid) load

PCR- Thermocycler
Takes “one” piece of DNA and makes many, many, many copies of it.
Often called a thermos cycler as to maximize the replication cycle temperature is changed to allow the Taq polymerase to effectively bind and replication the strand.

PCR Testing
This molecular testing has to be performed if detection of a viroid is the goal
This can also work for viruses.

RT-LAMP- Reverse Transcription Loop-mediated Isothermal Amplification
Loop-mediated isothermal amplification (LAMP) is a DNA amplification method that allows rapid and sensitive detection of a specific gene.
LAMP merged with reverse transcription (RT-LAMP) has been successfully used for the detection of several respiratory RNA viruses.
Uses a different enzyme than PCR that offers the advantage of being effective at one temperature and not a cycling of temperatures.

Field Testing
RT-Lamp: Similar to PCR that uses a specialize enzyme to amplify the viroid if present.
Downfall- Less sensitive
Good at finding positives, not as good at detecting true negatives

Antigen Testing
This tests for proteins so it can not be used for Viroids (unlike viruses)
Which One Should I Choose?
PCR is the standard for a reason and is considered to be the most reliable and also provides quick results.
It does not need a high number of viroids present in the original sample (technically it would only need one present) and it would still come back with a positive indication.


Link to Lecture Slides: https://drive.google.com/file/d/1R7Ss...

*Due to the description character limit the full work cited for "Comparing PCT to RT LAMP for RNA Detection and the Important for Hop Latent Viroid" can be viewed at... https://docs.google.com/document/d/1M...