Some COVID viruses share a concerning mutation. Now it’s cropping up in South Florida
When Miami researchers began examining the genetic structure of the COVID virus in local hospital patients about two months ago, they were impressed by the diversity of the strains — lineages traced from all over the world surfacing in South Florida.
But over the last several weeks, researchers have homed in on one trait that has become increasingly prevalent in viral samples taken from patients at Jackson Health System, Miami-Dade County’s public hospital, and UHealth Tower, the University of Miami’s hospital.
The E484K mutation, also known as the “Eek” mutation, is a structural change in the “spike protein” of the virus — the part that facilitates entry into human cells. One of the defining characteristics of the COVID virus variants that first took off in South Africa and Brazil, the “Eek” mutation is thought to allow the virus to more easily infect people who may have waning immunity from an infection, or a less than robust response to the vaccine.
Much of the attention to changes in the COVID virus has focused on the “U.K. variant,” which has become the predominant version of the COVID virus in Florida, as scientists predicted months ago.
Scientists think that the U.K. variant gained an advantage against other versions of the virus because it is more transmissible — perhaps via longer periods of contagiousness.
The COVID virus variants with the “Eek” mutation, on the other hand, gain an advantage through what is called an “immune escape” property, posing an entirely different challenge, and a question that will become more central to the fight against COVID as more people become vaccinated, and the virus continues to evolve.
Dr. David Andrews, a UM pathologist who is leading the university’s study on COVID virus mutations, said his team has noticed a “significant increase in lineages carrying the E484K mutation” as it examines more versions of the variants.
Rather than focusing their concern on a particular lineage, such as the “P1” Brazilian variant, Andrews says his team is now keeping their eyes on the “Eek” mutation and how it crops up in various places. He noted that the mutation has been tagging along with the U.K. variant, first observed in the United Kingdom, and, more recently, in Oregon.
“I think that is something that is going to be concerning in terms of public health, and is going to change the conversation a little bit away from a particular lineage,” Andrews said.
Andrew Pekosz, professor of molecular microbiology and immunology at Johns Hopkins University’s Bloomberg School of Public Health, said he agreed that the E484K mutation was beginning to “pop up in viruses of very different backgrounds, as if all the viruses in the world have figured out that this is going to help them.”
“Now, we have to figure out why it’s going to help them,” Pekosz said. “ ... It’s no longer a variant that we’re worrying about. It’s any virus out there that is picking up the E484K mutation.”
Bill Hanage, an epidemiologist at Harvard University’s T.H. Chan School of Public Health, noted that it’s not just how often researchers are finding the “Eek” mutation, but where they are finding it.
“It has been popping up all over the place in locations where there has been substantial transmission recently, together with a history of many previous infections,” Hanage said, a phenomenon he attributed to some degree of immune evasion.
“It is turning up everywhere, and getting more common through the ability to reinfect people who have recovered from their first bout with the virus. While the characteristics of such reinfections in comparison with the first round are not clear, they are obviously worth taking seriously.”
Watching for ‘breakthrough’ cases
Though the vaccines are still thought to be largely protective against even the COVID virus carrying the “Eek” mutation, scientists interviewed by the Miami Herald said the structural change in the virus is likely to increase the potential for reinfections or, separately, “breakthrough” cases — people testing positive for COVID-19 even after completing their vaccination series.
Both reinfections and breakthrough cases are to be expected with any virus, scientists agreed, and few vaccines are 100% effective. Additionally, every person’s immune response is different. But there is still a lot unknown about both the durability of the vaccines and natural immunity to COVID.
There is reason to be optimistic. Pfizer and BioNTech on Thursday said their vaccine is 100% effective in preventing COVID cases against the South African variant, which features the “Eek” mutation, and that protection lasts at least six months.
John Moore, a virologist at Weill Cornell Medical College in New York City, said the COVID virus spin-offs most closely monitored by scientists are called “variants of concern,” and not “variants of mass panic,” for a reason.
“We don’t know the degree of [vaccine] resistance,” he said. “It’s not like people should panic and say the vaccine isn’t going to work. It just increases the probability of the problem.”
The Florida Department of Health is monitoring for such breakthrough cases, and has already recorded some, but it’s unclear how often the department is analyzing the genetic sequences of the virus in people who get infected despite having received a vaccine.
Andrews, the UM researcher, says such cases should all be closely examined.
“That needs to be a structured effort,” he said. “ ... Every single one of them needs to be sequenced.”
The Department of Health did not respond to a request for comment on its efforts to monitor breakthrough cases. It’s unclear how many have been recorded in South Florida.
Are Florida’s rising COVID cases due to the variants?
Following a national trend, Florida experienced its “third wave” of COVID cases over the winter, peaking in mid-January, leading to a surge of illness and death just as vaccines were getting to the state’s most vulnerable.
In late January, the surge began to recede, and declining case levels gave public health experts hope that widespread vaccination could help keep hospitalizations and deaths from the virus low.
So far, that has borne out, but the COVID virus is still circulating in high levels throughout the state, especially in Miami-Dade, where there are 44 daily cases per 100,000 people — the U.S. Centers for Disease Control and Prevention considers anywhere between 5 to 50 daily cases per 100,000 people “moderate” spread. Anything above that is considered “high” spread.
In various parts of the state, cases are rising — and fast.
Orlando’s Orange County, for example, has seen a 62% increase in cases among college-aged people (18-24) compared to two weeks ago. Additionally, there has been a 35% change in the 25-49 age bracket in that time, and, most concerning, a 42% rise in the 50-64 age bracket, according to an analysis by University of South Florida professor Jason Salemi, who closely tracks Florida’s COVID data.
In Miami-Dade, the case increase is more concentrated in those under 50, especially the college-aged. Over the last two weeks, cases in people 18-24 have increased by 39%, Salemi said. But in Broward, case increases have been increasing across age brackets, including the 50- to 64-year-olds, who qualified for the vaccine about two weeks ago, and saw a 13% increase in cases.
Statewide, cases are still dropping for those 65 and older, which Salemi attributed to vaccines. Hospitalizations from the virus have remained flat after a period of decline, with about 3,000 people being treated for COVID in Florida on Thursday morning.
“In general, we’re seeing pretty pronounced increases in those individuals who are 18 to 49 years old, but particularly the college-age group,” Salemi said, emphasizing that the case rates vary significantly by county.
Salemi attributed the case rise to spring breakers, COVID fatigue, more-infectious variants and relaxing mitigation efforts.
Most urban counties, including the Tampa Bay counties of Hillsborough and Pinellas, are seeing cases rise. But in Jacksonville, which had one of the most significant winter surges, cases are still decreasing across all age groups.
Researchers are confident that mutated versions of the virus are becoming increasingly common due to natural selection, but there isn’t enough data to determine just how much that is driving case increases across the country, including in Florida, where the more transmissible U.K. variant has been racing to become the predominant strain, according to estimates.
Natalie Dean, a biostatistician and assistant professor at the University of Florida, noted that several different parts of the U.S. are witnessing case rises.
“Their timing is all a little different, and some places, like Michigan, are a bit further along in their trajectory, but they are starting to see a rise in hospitalizations,” Dean said. “The hope is that vaccination of the elderly will go a long way in reducing hospitalizations and deaths, but just because one segment of the population is better protected, another segment remains vulnerable.”
Dean added that there is compelling data from the U.K. that the B.1.1.7 variant is not only more transmissible, but also more severe.
“I’ll be paying attention to what happens in younger adults,” she said.
High caseloads also give the virus more chances to mutate
The more the virus circulates, the more likely it is to acquire new mutations, including on top of existing mutations, scientists told the Herald.
It’s the way viruses typically evolve — through selective advantage, said Pekosz, the Johns Hopkins researcher.
“It may only be a one-in-a million chance that a virus mutates, but we’ve let the virus roll the dice 900,000 times,” he said. “Now you’re seeing the results of that.”
As the virus evolves to get more fit, Pekosz warned, many of the initial calculations have changed about what would be needed for “herd immunity,” or the threshold of vaccinated and previously infected people great enough to stop the virus’ circulation.
“These mutations now, they are changing the properties of the virus, so we have to go back and rethink our concept of herd immunity,” Pekosz said. “It may be that we need either a higher level of herd immunity now to deal with these variants or we may need to tweak the vaccine to get a different type of immunity and make sure we’re more broadly covering the new variants that are coming out.”
Mary Jo Trepka, an epidemiologist at Florida International University who advises South Florida officials on the virus, said it’s important to remember the vaccines are incredibly effective, including against the variants, especially when looking at breakthrough cases.
“Four hundred thousand people have gotten the vaccine [in Miami-Dade County],” Trepka said. “Ninety percent of them are going to be protected based on normal response. That means a certain percent aren’t.”
Trepka said Miami-Dade’s recent caseload was likely due to a mix of behaviors around spring break as well as some influence from the variants circulating here.
“Even with the ‘Eek’ mutation, the vaccine still has value,” she said. “It’s still efficacious. It’s just possibly less so.”
Andews, the UM researcher studying mutations, said it was still too early to determine whether the rise of the “Eek” mutation in Miami-Dade had to do with its ability to escape prior immune responses. But, he added anecdotally, he has been fielding more phone calls recently about potential reinfections.
What worries him most, Andrews said, was the propensity of the “Eek” mutation to attach itself to other lineages, particularly more-contagious ones such as the U.K. variant.
While the mutation is a hallmark of antibody resistance, Moore, the Weill Cornell virologist, said that doesn’t give the virus superpowers. Even people who get reinfected due to a variant are unlikely to die from that reinfection, he said, especially if they have been vaccinated.
“This is not a knockout; it’s a degree,” Moore said. “It’s a shade of gray. It’s not black and white.”
This story was originally published April 1, 2021 at 11:40 AM.
