Q&A: Developing a test to detect new COVID-19 variants

Milan Patel, CEO and co-founder of Pathogen Dx spoke to Med-Tech Innovation News about developing technology to detect COVID-19 variants, which tests can detect variants and building an efficient system. 

Tell us about developing a technology that goes into detecting a new variant. What kind of work goes into it?

We are constantly scanning three databases, those of the World Health Organisation (WHO), GISAID and Rosalind (NIH, CDC, FDA), that monitor certain sequences of mutations of the virus. As the percentage of occurrences increases, WHO and CDC categorise them into Variants of Interest, Variants of Concern and Variants of High Consequence. The categorisation of these variants allows us to determine if the mutations are covered under our current Detect^x-Cv test; if they’re not, we add in the probe(s) necessary for us to test for that mutation. Then we have to make sure the chemistry -- primers and reagents -- works with the new mutation. This approach is similar to that of other diagnostic companies, the only difference being that our approach takes a fraction of the effort.

You say that all major variants are detected, how do you tweak your technology when a new variant comes along?

Our tests have a certain number of probes in our arrays that are printed at the bottom of each well in a 96-well plate. Each variant is defined by specific mutations that we have designed into our assay from a probe and primer perspective. The probes in our wells define the mutation present on the spike protein of SARS-CoV-2.  When a new variant comes along, we add in new probes as necessary and check if current primers work, making adjustments as needed. In the case of the new Variant of Interest, Mu, we did not need new probes or adjusted primers. Our current assay already detected mutations of the spike gene that represented this new variant so all it took was a quick software change to the call algorithm and the assay to test for Mu was instantaneous.

Where do you currently have a footprint? Do you have a presence in the UK and Ireland for example?

Our tests are used by small- and medium-sized CLIA and clinical labs in the U.S. as well our clinical validation sites, such as the Stanford Virology Department, TriCore Reference Labs and University of Miami. We are not in the UK or Ireland but we would love to partner with clinical CLIA labs and organisations testing for COVID variants within those countries.

What differences are there in your technology compared to standard COVID tests that detect infection that everyone is more accustomed to?

Our technology leverages multiplexed testing on our patented microarray and utilises endpoint PCR technology for much greater sensitivity and higher accuracy at a fraction of the time and cost of qPCR and NGS. The benefit of using a microarray is the ability to target COVID-19, Influenza, RSv and other respiratory pathogens all in a single swab. The test can detect even very low levels of infection with high accuracy. Lastly, the technology uses standard everyday lab equipment that basic lab technicians are already familiar with, so training is minimal. Reporting does not require specialised bioinformatics like sequencing does.

In terms of our COVID-19 variant test, we can test multiple targets on the virus. Our Detect^x-Cv tests for COVID-19 at 14 different sites for more certainty and confidence in the test result itself. The turnaround time is roughly four hours versus four to ten days minimum for sequencing, and is $125 to $475 less expensive than other tests on the market.

Anything else you’d like to add? 

Over the past 18 months, we’ve moved from one evolutionary phase of testing to the current phase where we need to test not just for the original virus but its variants, as well. There are now many different flavours of variants circulating throughout society, each with different impacts on an infected individual in terms of treatment and vaccine effectiveness.

This virus is not going away. It is important that we understand comprehensive COVID-19 testing from a diagnosis perspective and an epidemiological and public health standpoint. By developing a technology that both diagnoses and collects vital information, we have not only flattened the curve but also compressed the three-week process of getting critical clinical and public health information down to one to two days.