How Major League Baseball is tracking COVID-19 variants

To play during the pandemic, Major League Baseball has stepped up to the plate.

The league is using coronavirus tests in a new way that allows them to determine not only if a player has COVID-19 but also if a variant of the virus caused the player’s infection.

The MLB is one of few professional sporting organizations that is starting its second season in the coronavirus pandemic.

After a few high profile COVID-19 outbreaks among different teams last season, the league used a saliva test to track cases of COVID-19. The MLB identified 89 positive cases after outbreaks on different teams, and frequent testing ultimately reduced transmission among players and staff.

But new COVID-19 variants have thrown a curveball in their plans this season.

“MLB is a microcosm of the US and so we absolutely are seeing different variants, as you would expect in the regular community as well,” Daniel Eicher, president of The Sports Research and Testing Laboratory told CNN Chief Medical Correspondent Dr. Sanjay Gupta in a recent interview.

Variants throw a curveball

The MLB is working with Eichner and his lab to detect variants in ball players using a coronavirus testing method called “alternative variant analysis.”

To test for variants, scientists typically have to sequence all of the coronavirus’ genetic material. The process is costly and time consuming, which can take days or weeks to get results.

Such delays have inhibited the ability to quickly and accurately contract trace positive cases to help experts understand the true magnitude of any concerning COVID-19 variant spread in the US.

Eichner’s method needs to see much less of the virus to make a determination.

“Our variant analysis program specifically looks for a certain region on the virus that we know that mutations are indicative of the different variants that are known, Eichner told Dr. Sanjay Gupta in a recent interview.

Variants are defined by their mutations, and it is typical for viruses to mutate. There are hundreds of variants of the novel coronavirus, and the vast majority of mutations are harmless to humans. But some mutations can make the virus more transmissible, more deadly or even resistant to vaccines and therapeutics.

The major benefit of Eichner’s variant analysis methodology is that it relies on polymerase chain reaction, or PCR tests, that are already being widely used to detect the virus. With an adaptation, the test can also give real-time results on whether a variant caused the infection.

It doesn’t give the full picture of the variant like genetic sequencing does, but it’s a much quicker screening tool.

“We can do it in real time, the same day we received the samples, we’ll run that analysis and let them know,” Eichner said.

Beyond baseball

Alternative variant analysis could potentially be incorporated into COVID-19 testing more broadly to get a better handle on where variants are spreading in the US.

A recent Yale study found that this PCR screening method could act as an urgent “surveillance tool to help monitor the distribution and population frequency of suspected variants.”

Using PCR tests to analyze variants is one of the reasons so many cases of the UK variant have been found because the variant causes a glitch on one type of PCR test that tipped scientists off , according to Dr. James Lu, president of a company called Helix, whose COVID-19 tests have helped identify many of these cases.

“This gives you a very good result immediately, and that can help you drive your public health policy,” Eichner told Gupta.

And that’s an important point. Right now the US doesn’t have a good picture of how much the variants are spreading because not enough surveillance is being done—the US only sequences 4% of coronavirus cases, according to comments by CDC Director Dr. Rochelle Walensky in a March 25th event hosted by the Pandemic Response Accountability Committee.

Broader use of the new method might help.

“It’s a useful strategy, it can be used very mindfully and be used on a fairly large scale if we use it correctly,” a CDC official told CNN when asked about the alternative variant analysis testing methodology.

One concern is that the PCR analysis only identifies variants that have already been discovered, so it doesn’t necessarily tell experts where the new, undiscovered bad strains are, the official told CNN.

But if experts could have a better idea of what strains are spreading in our communities, the US has a better chance of getting and keeping this virus under control — and preventing future outbreaks.

“I think that this information would be extremely valuable to health policy makers for sure,” Eicher told Gupta. “There’s nothing to lose by doing this, all the labs testing for SARS-CoV-2 to right now, they’re all using PCR technology so there’s no reason why they couldn’t incorporate this kind of technology.”