CDI researchers helping doctors stay one step ahead of variants — for now

There’s the U.K. variant, another for South Africa, one for Brazil — and a few from the U.S. But, here’s the money question when it comes to variants: Do doctors fear there will soon be a variant for COVID-19 that the current batches of vaccines do not protect against?

On the day the Center for Discovery and Innovation — the real-time research arm of Hackensack Meridian Health — announced it has created an assay that can determine COVID-19 variants in a patient in as little as two and a half hours, we asked Dr. David Perlin, the director of CDI, this question.

The answer: There’s always a fear. And, while it’s not a major concern today, it could be tomorrow.

It’s one of the many reasons that CDI worked quickly to create a high-speed test for identifying specific variants.

“Of course, it’s a fear,” he said. “There is a concern that we’re going to have virus variants that will overcome the immune system. We have not seen that yet in terms of the vaccine.

We’re hopeful that that will not happen — and I think it’s unlikely. But, frankly, this virus never ceases to amaze me. It’s always one or two steps ahead of us, so we have to stay vigilant.”

Perlin and the doctors and scientists at CDI are trying to stay ahead of the variants. They aren’t alone.

“I can tell you that Pfizer, Moderna, J&J and others are already working on the next-generation vaccine, which will be that much more effective against viral variants,” he said.

“The good news is that we already have really sophisticated tools available to us to help us able to keep pace with the virus and the variants.”

CDI, of course aided the fight with Thursday’s announcement of the latest tool, the quick-turn variant test. (See full story here.)

With that as the background, ROI-NJ talked with Perlin concerning all things variants. Here are his thoughts, edited for space and clarity.

ROI-NJ: Why is the quick-turn test so important when it comes to fighting those with the variants of COVID-19?

David Perlin: The variants dictate therapy. For people who are presenting to emergency departments, we often use antibody cocktails made by Lilly or Regeneron. We now know that the E484K mutation, which is the centerpiece for the Brazilian and South African variants, is actually less sensitive to those antibodies.

It’s really important to detect variants and understand what we’re dealing with. Our doctors need to know what is happening in real time.

ROI: When did you decide you needed to create a faster variant test — and how long did it take to create one?

DP: In December, there were reports of these rather significant variants of concern in Brazil and South Africa that were causing reinfections and were being classified as immune escape, which means it allows the virus to circumvent the immune system. And then, there was a lot of discussion about the U.K. variants sort of taking over the virus population in the United Kingdom.

That’s when we became concerned, and we realized that we couldn’t use whole genome sequencing. It was just too slow a procedure. In mid-January, as we started analyzing viruses that were coming through our network, we knew we needed a better approach.

Once we decided that we needed a higher throughput assay, it took about two weeks to design it, test it and put it in place.

ROI: The test you’ve created has a 2.5-hour turnaround. How long was it taking?

DP: At least 24 hours. Whole genome sequencing is a very demanding process. There’s a lot of preparation time and it’s not always easy to get enough RNA to be able to do sequencing. So, it’s not very efficient. It takes at least 24 hours. And, in most cases, it’s two to three days to get turned around. And you’re lucky if you can get 10 or 20 viruses to sequence. We now can do hundreds in a day.

ROI: Are all of these variants surprising — or was it what you were expecting?

DP: We knew this was coming. It’s a natural process. The virus has been evolving since the beginning. It is trying to overcome the immune system, so it selects for mutations, which allow it to circumvent the immune system. That’s exactly what we’re seeing.

ROI: We hear about the U.K., South African or Brazilian variant — is there a U.S. variant?

DP: There are U.S. variants. For example, some of the variants we’ve seen with E484K in New Jersey are the so-called New York variants. It’s not U.K., it’s not Brazilian, it’s not South African. It is a variant that has evolved in New York and is spreading quite readily in the New York region. California has its own variant.

I think what we’re learning is that, each region, as far as what evolves, there are certain viruses that just sort of take off in that region.

ROI: Last question: As an expert in this field, what does the public need to know about variants?

DP: We have to stay vigilant. Because there are variants, and they have the potential to be more dangerous, people have to protect themselves. Infection control measures, such as masking, have to be really strictly adhered to.

And we need to vaccinate. By getting vaccinated, you put yourself in a completely different category and are much better off to fight a reinfection and certainly to protect yourself long term.