Tracking New COVID-19 Variants with Bioinformatics

Paul Oladimeji
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How continued surveillance and testing will help manage potential outbreaks of new variants

Paul Oladimeji, PhD, is a researcher specializing in PCR technologies and is currently the head of product development at Novacyt Group. His previous experience includes investigating DISC1 molecular pathway disturbances in major psychiatric disorders and identifying cis-regulatory variants in AKT1, a schizophrenia candidate susceptibility gene. Paul’s many years of experience and expertise helped Novacyt Group launch one of the world’s first gold standard COVID-19 test kits to assist in managing the pandemic.

Q: WHAT DIFFERENTIATES NOVACYT GROUP’S COVID-19 DIAGNOSTIC PRODUCTS FROM OTHERS ON THE MARKET?

A: We have over 500 products detecting a variety of pathogens. Each product will detect a disease-causing microorganism, microbe, or virus. We have this range because our customers need products to detect some diseases that aren’t as well served by the molecular diagnostics space, such as neglected tropical diseases.

Our expertise in covering such a vast range of pathogens allowed us to be first movers in making a product for SARS-CoV-2 detection. The speed with which we developed the product meant that we were the first to offer a diagnostic for SARS-CoV-2 in Europe, the second to be approved by the WHO, and the fifth to be approved by the FDA.

The unique thing about our products is that we designed them to be able to be used on a variety of instruments. We are system agnostic. We have a big catalog of products that extend beyond your typical 10 or 20, which are designed to work on our own qPCR instruments and the instruments of other suppliers. So, if you’ve got a lab and if you’ve got a qPCR instrument, our products can benefit you.

Our FDA-approved product for SARS-CoV-2 has a number of distinguishing features. One is that it can be automated, or you can do a manual extraction. Our products have been validated as being compatible with an automated system for those with high-throughput, mass-automated labs. We’ve also got a manual extraction product for laboratories that don’t have those automated systems.

Q: HOW HAVE YOUR PRODUCTS PERFORMED ON THE COVID-19 VARIANTS?

A: The product isn’t just the assay that turns up at the door, and I think that’s something people in labs need to understand. Pathogens don’t just stand still. You’re dealing with dynamic systems and for the entire year that our products have been in the field, the SARS-CoV-2 virus has been evolving. Not everyone is familiar with it now, but we were one of the first back in April 2020 to start publishing our bioinformatics surveillance. Since we launched our diagnostic, we publish weekly bioinformatics data that says, “This is what the virus is doing, and our product will still detect it.” We are still detecting all the SARS-CoV-2 variants that are out there with our product.

If there was one unique thing that we were doing for our products, aside from launching them before our competitors, it would be doing the bioinformatics surveillance with real statistical rigor before it became sexy and everyone was doing it.

The variants are very interesting because they capture the public’s imagination. The variants are happening all the time; every day there’s a new variant, but is that variant going to be of any significance? Most of the variants arrive and you probably never see them or hear of them or encounter them because they don’t offer any biological benefits, so they just mix in with the general population and any mutations that define that variant won’t last long in the next generation or the next wave. But we’ve been tracking all of those, and when you include all of the sequences that have been published, we cover 99.8 percent of all of them with no mismatches. We still predict we’ll detect the ones where there are mismatches, and we’ve done in silica modeling and actual wet lab experiments on versions of variants that have mismatches under our primers and probes and demonstrated that we can still detect them. So, we’re talking about bioinformatic surveillance on a level that has never been industry standard, but we’re really proud to be setting the standard.

Q: HOW DO YOU SEE THE NEED FOR THESE DIAGNOSTIC TESTS CHANGING IN THE NEAR FUTURE?

A: Of course, you hear in the industry about the COVID plateau, but I think it’s going to be a high plateau. COVID is not going away—it is going to be with us for the foreseeable future and it’s going to be something that we’re going to need to manage, just as we do with flu. COVID testing will allow us to keep track of any new waves and manage any necessary safety measures that need to be put in place with a risk-based approach. You don’t want to be making these decisions based on a gut feeling—you need data, you need to track it, and the COVID-19 test will help protect the entire population by allowing us to manage any potential outbreaks of new variants in the future.

Paul Oladimeji, PhD
Paul Oladimeji, PhD