Scaling Up Primer and Probe Kits for COVID-19 Testing

As the COVID-19 pandemic unfolds, efforts are underway to rapidly increase testing capabilities, to help identify infected individuals and try to limit the spread of the virus. On February 4, 2020, the US CDC’s testing protocol [CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel] received Emergency Use Authorization (EUA) for the diagnosis and detection of COVID-19. This protocol relies on a number of components, including specific primers and probes.

Integrated DNA Technologies (IDT) recently became the first company in the US to receive approval for their primer and probe kits to be used as a key component of this testing protocol and has successfully scaled up production of these kits. Starting from March 16, 2020, they expect to manufacture enough kits to enable five million tests to be performed in the US per week pursuant to the CDC EUA testing protocol.

Technology Networks spoke to Trey Martin, President, IDT, to find out exactly how primers and probes work, and learn about the important role they can play in COVID-19 testing.

Anna MacDonald (AM): Why is it so important to increase the availability of COVID-19 testing?

Trey Martin (TM): One of the most important steps in fighting emerging pathogens is identifying infected patients. This can be complicated by pathogens with longer incubation times or symptoms that are not distinct from common, non-threatening infections.

Obviously, failure to identify and treat infected people increases the risk and rate of the disease spreading. Additionally, patient observation and treatment regimens based on false-positive assessments lead down blind alleys and result in a waste of precious time and resources. Therefore, the establishment of diagnostic methods accounts for a large part of early research activity around potential pandemics. Fortunately, researchers have gained a lot of ground on the diagnostic front over the past few decades.

AM: Where does IDT’s primer and probe kit fit into the CDC’s COVID-19 testing workflow? What do the primers and probes do?

TM: IDT makes a kit containing DNA primers and probes that are designed to amplify and detect the presence of specific viral RNA in a patient sample, in this case, sequences that are specific to COVID-19 coronaviruses.* If a patient sample contains COVID-19 coronaviruses, the DNA primers will amplify (make billions of copies) those virally derived DNA sequences, and the DNA probes will fluoresce (or light up), allowing the instrument (a special thermocycler) to detect and quantify that fluorescent signal. That patient would be positive for the COVID-19 coronavirus. If the patient sample contains no coronaviruses, the DNA primers will not amplify any sequence and the probes will not fluoresce (will remain dark). That patient would be negative for the COVID-19 coronaviruses.

For the IDT-made DNA primers and probes to work in this manner, they must be used in concert with a special reaction mixture called a "master mix", which includes a class of enzymes called polymerases. The polymerases and the DNA primers drive the amplification reaction (the making of the billions of copies of the virus-derived cDNA) called the "polymerase chain reaction”, or PCR. For the fluorescence from the DNA probes to be detected and quantified, the DNA primers and probes, along with the polymerases, must be used on a special "quantitative PCR" instrument, which is capable of detecting and measuring the amount of fluorescent signal generated during the qPCR reaction. These kits made by IDT contain only the DNA primers and probes—other vendors make the extraction reagents, the master mixes and the qPCR instruments. 

* Coronaviruses are RNA viruses. the RNA is copied to DNA (i.e., cDNA).

AM: How did you achieve rapid scale up of the kit, and what challenges did you face in doing so?

TM: IDT is accustomed to cyclical demand (for example, the regular flu season), so it is prepared to reassign cross-trained staff and has standard processes in place to accelerate acquisition of raw materials to respond to spikes in demand.

For example, IDT’s recent history includes providing products to diagnostic test manufacturers developing tests for H1N1, Ebola virus, and Zika virus. This experience made IDT well-positioned to help increase the availability of COVID-19 testing by being the first company in the nation to have our primer and probe kits approved by the CDC for use as a key component of the CDC EUA testing protocol for the diagnosis and detection of COVID-19.

As of March 23, 2020, IDT had shipped primer and probe kits sufficient to enable more than 10 million tests to be conducted in the US pursuant to the CDC EUA protocol.

AM: In what other ways is IDT working to support the coronavirus outbreak response?

TM: On February 10^th, IDT released a primer and probe kit for COVID-19 research and offered preferred pricing and early access to the global health and research communities.

The US CDC and FDA first contacted IDT on February 25th to discuss its ability to support the CDC EUA testing protocol. IDT shipped primer and probe kits to the CDC the same day for delivery on February 26th. On March 2nd, the FDA included IDT lot#0000500383 as the first primer and probe kits qualified under the CDC’s EUA. Subsequently, the CDC has continued to qualify additional lots.

Trey Martin was speaking to Anna MacDonald, Science Writer, Technology Networks.