How Connecticut researchers search for virus variants.
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Viruses mutate. Most of the time, those mutations don’t benefit the virus. Sometimes, those mutations help the virus in some way and it branches off into a new variant, genetically distinct from others of its kind.
In the case of the variant known as B.117, originally identified in the United Kingdom, its mutations make it about 50 percent more transmissible though no more deadly than the original coronavirus that so far has caused more than 6,000 deaths in Connecticut.
It’s been more than a week since that COVID-19 variant was first confirmed in Connecticut and, as Mary Petrone indicated, she and other researchers believe it was in the state since sometime in December.
Petrone is a doctoral candidate at Yale, working as part of a team that has been doing gene sequencing of the coronavirus since the very start of the pandemic. She’s the one who walks the samples from the pathology lab to the machine that does the genomic sequencing.
“It started coming onto our radar at the beginning of December, like everybody else, when the U.K. was starting to look at it,” she said.
Around Christmas, they decided to “ramp up surveillance” for the new variant, “because, I mean, it was almost definitely here. So, we thought, ‘might as well get out ahead of it and try and try and identify it.’”
They found it on Jan. 6. Between the time she picked up the sample and when they identified the variant was less than two full days.
“I think it was Tuesday afternoon, I went and picked up the RNA sample from the pathology lab,” Petrone said. “To prepare for sequencing, it’s usually like a day-and-a-half process.”
By Wednesday, they had confirmation that the B.117 variant was, in fact, spreading throughout the state.
“In that case, it was a really quick turnaround time,” Petrone said. Her colleague, Tara Alpert, read the data as the sequencer worked.
“The sequencer that we use in the lab, you can actually pull data off as it’s going,” Petrone said.
It helped that they knew what to look for. The B.117 variant hides itself in a tricky way, but the manner of its camouflage helps people like Petrone find it.
One of this variant’s mutations is a missing protein, one of the three parts of the virus targeted by commonly used coronavirus tests. It doesn’t mean that every sample with that deletion is the B.117 variant, but it provides a clue.
“You get this really weird profile that people were noticing where two of the targets are really, really positive,” Petrone said. “And then you just have no signal at all in the target in the spike protein.”
So, how widespread is the variant now?
“My sense is that it’s still at a low level right now, which is really good news,” Petrone said. “I can’t definitely put a number on prevalence. I would say it’s probably low. And I think that we should expect it to increase in the next couple of months pretty dramatically.”
Eleven states had confirmed a total of 76 cases of the B.117 variant in the United States as of Wednesday, according to the CDC, 32 of them in California. There have been a total of two found so far in Connecticut.
On Friday, the CDC said it “and other federal agencies are coordinating and enhancing genomic surveillance and virus characterization efforts across the United States.”
The agency’s weekly report said to expect wider coronavirus spread as a result of the variant: “Modeling data indicate that B.117 has the potential to increase the U.S. pandemic trajectory in the coming months.”
The United States, Petrone said, has done less genomic sequencing of the coronavirus than other countries though now, with the increased danger of B.117, there will be more sequencing in the future.
“At least in the U.S., it’s very few, especially compared to the U.K.,” she said. “I think that is probably going to change, now that we understand the importance of it. But it’s definitely very few.”
As for why so few samples are sequenced in the United States, Petrone said cost was definitely a factor.
“It is pretty resource intensive. It’s not just something you can pick up casually. It costs a lot of money, you need trained personnel to do it. You really need to make a concerted effort to do it.”
But there’s also a question of focus. There has not been a centralized push from the federal government, according to Petrone, with regard to lockdowns, coronavirus testing, use of masks or genomic surveillance.
“I think that that makes a big difference,” she said. “Because if you don’t have a unified response, then you’re sort of relying on labs like ours, which again, is a really small research lab that’s just doing this because we’re able to and we have time. Other than that, you’re sort of just hoping that others could do it.”
B.117 is not the only coronavirus variant currently circulating. Another, called B.1.351, was originally identified in South Africa. Another was recently identified in Brazil. Neither have yet to show their faces in the United States.
“I think we’re just being vigilant for, you know, the South African, South American (variant), all these ones that are in the news,” Petrone said. “Our goal in establishing a more robust genomic surveillance system is to not only track the spread and the prevalence of the B.117 variant, but also to look out for new ones.
“We don’t know what those would be, and we don’t know how they would impact any sort of epidemiological relevant factor, but we are keeping an eye out for any new variants, good or bad.”
Because, again, viruses evolve. Petrone and her team, led by Yale School of Public Health assistant professor of epidemiology Nate Grubaugh, are not the only ones in Connecticut monitoring the coronavirus as it changes, but they are maybe doing the most to track it.
As Yale School of Medicine’s medical director for infection prevention, Rick Martinello, explained, the coronavirus is an RNA virus, which mutates faster than DNA-base viruses.
“It’s within their nature to have very frequent mutations,” he said. “Those mutations are either what we call a ‘silent mutation,’ meaning it doesn’t do anything to the virus, the virus doesn’t behave any differently, or that mutation is actually deleterious to the virus.”