In an attempt to increase the Coronavirus (COVID-19) testing capacity, the FDA provided emergency authorization for many new tests including two commercial tests from Roche and ThermoFisher. This article describes the automated Coronavirus testing technology employed.
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What are the COVID-19 (Coronavirus) tests?
We had originally planned on giving an in-depth review about the COVID-19 tests, but Wired beat us to it with their article “Everything You Need to Know About Coronavirus Testing“. Rather than writing another testing article review, we suggest you read the Wired article. The description of the science is quite good and we will use it as our starting point.
As the Trump administration announced on March 13th, the FDA has given approval to Roche and ThermoFisher for their Coronavirus infectivity tests. Both of those tests are high throughput and automated by design.
There are a total of 28 tests available in the US market. There are also over 110 tests that currently used in independent labs. All of these tests fall under the FDA’s emergency authorization.
How well these different tests work is not actually something that is easy to determine since the FDA has not yet viewed the validation data for all these tests and that may be a story for a different time.
We will focus on the technology employed to make the high throughput tests possible including:
- Reverse Transcription quantitative polymerase chain reaction (RT-qPCR): Real time PCR thermal cycler
- RNA extraction: RNA extraction kits, liquid handling robots
- All in one systems: Roche Cobas 6800/8800 , KingFisher Apex, QiaSymphony
What is a real time PCR thermal cycler (qPCR) anyway?
qPCR machines work by cycling through a series of temperature set-points in a process designed to rapidly replicate deoxyribonucleic acid (DNA) sequences. “Real time” or “quantitative” PCR is possible because of an integrated fluorescence detector. This integrated detector measures fluorescence as the nucleic acid replication occurs. fluorescence intensity increases indicate that the DNA sequence is present.
Coronaviruses, use ribonucleic acid (RNA) instead of DNA; The Coronavirus RNA needs to be reverse-transcribed (RT) into DNA before the DNA can be replicated through qPCR (Reverse Transcription Quantitative PCR – RT-qPCR).
There are many real time PCR (qPCR) systems on the market. Most biotech and molecular biology labs have at least one system of the following systems.
- AriaMX Real Time PCR (Agilent)
- CFX96 Touch Real-Time PCR (Bio-Rad)
- LightCyclerTM 96 (Roche)
If you are wondering where the RT-qPCR is occurring, you are not alone. Quantitative PCR instruments accept samples in a 96-well PCR plate. Each of the 96-wells of the PCR plate typically holds 20 microL of volume. Fluorescence is continuously measured in each well simultaneously allowing all wells to be analyzed in parallel in under an hour.
How to automate RNA extraction?
RNA extraction from a Coronavirus usually includes the following:
- Detergent to break the lipid bilayer envelope if the virus
- Denaturant to inhibit RNAses from degrading the RNA
- Reverse transcriptase to transcribe the RNA into DNA
- DNA polymerase to amplify DNA from the transcribed DNA
- Primers specific for Coronavirus RNA transcription and DNA amplification
Liquid handling robots perform the liquid addition of the components. Systems equipped with manipulator arms can also perform the physical sample manipulations required to initiate RT-qPCR. Each robot in the liquid handling robot list can be programmed to perform RNA extraction. However, the Hamilton STAR, Beckman BIOMEK, and Tecan EVO systems tend to be the systems most people are using currently.
Fully automated Coronavirus testing
An example of a fully automated RT-PCR system is the Roche cobas 6800/8800. They include integrated liquid handling robotics and a qPCR. Designed to test clinical samples, these instruments are used to test multiple infections besides the COVID-19 Coronavirus.
What is the 5 minute (quick)(fast) Coronavirus test?
Abbott Labs has developed a new 5 minute Coronavirus test on their ID NOW technology. The 5 minute assay is for positive results while a negative results takes about 15 minutes. This a great when you don’t have a large number of samples to test at the same time.
But the throughput of the ID NOW is around 4 samples per hour. This is much lower than the automated Coronavirus testing we have described above.
Automated, high throughput testing is essential as long as there is no vaccine
The United States is going to continue to need automated, high throughput testing for Coronavirus for the foreseeable future. We have a long road before there is a readily available vaccine or treatment. Testing and tracing outbreaks will be essential to ensure people they are not at risk of catching or infecting others.
The question is whether this capacity is here to stay; or is it just a blip due to the pandemic of the century. I believe that we are on the path to lasting change and life saving technologies beyond the current pandemic.
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