COVID Variant KP.3 (FLiRT) on the Rise Across the US: CDC

KP.3, is rising to become the dominant strain of the virus across the United States, according to the Centers for Disease Control and Prevention (CDC).

KP.3 constitutes about 25 percent of all COVID-19 cases detected by the agency. It’s followed by the KP. 2 and LB. 1 variants, which make up about 22 percent and 14 percent of all cases, respectively, the data show.

The latest COVID-19 data were collected over a two-week period from May 26 to June 8, 2024. Some media outlets have referred to both the KP.2 and KP.3 variants as “FLiRT,” due to where spike proteins are located.

“CDC predicts that KP.3 is growing and will become the most common SARS-CoV-2 lineage nationally,” a CDC spokesperson told several news outlets this week about the variant’s dominance. “CDC is working to better understand its potential impact on public health.”

But the data suggest that despite the increase in the KP.3 variant’s prevalence, the U.S. is currently seeing low levels of COVID-19 activity overall.

A CDC graph of COVID-19’s historic trends shows that weekly deaths are at the lowest point since the pandemic started in early 2020. Virus-linked hospitalizations are also at their lowest point, the data show.

“Most key COVID-19 indicators are showing low levels of activity nationally, therefore the total number of infections this lineage may be causing is likely low,” the CDC spokesperson said.

Andy Pekosz, a molecular microbiology professor at Johns Hopkins University, said that the KP.2 and KP.3 variants do not appear to be more or less severe than prior COVID-19 strains. Instead, most people have COVID-19 antibodies either through a previous infection or vaccines.

“The period of infectiousness for these FLiRT variants remains the same as with JN.1 and previous omicron variants: After exposure, it may take five or more days before you develop symptoms, though symptoms may appear sooner,” he said in a question and answer session that was published on the university’s website.

“You are contagious one to two days before you experience symptoms and a few days after symptoms subside. And as with previous variants, some people may have detectable live virus for up to a week after their symptoms begin, and some may experience rebound symptoms.”

COVID-19 Reports No Longer Required

Last month, the CDC said that hospitals will no longer have to report COVID-19-related hospital admissions, hospital capacity, or related information. The changes went into effect on May 1.

The old “data will be archived as of May 10, 2024, and available at United States COVID-19 Hospitalization Metrics by Jurisdiction, Timeseries,” according to a statement posted on the CDC website at the time.

But the agency still encouraged medical facilities to report COVID-19 hospitalizations and related information to the federal health agency.

“A key lesson we learned from the COVID-19 pandemic is the importance of having reporting systems in place before an active emergency,” a CDC spokesperson said.

“These data have a significant and ongoing value for protecting patient health and safety as well as public health,” the statement added.

A U.S. Food and Drug Administration (FDA) panel, which authorized every previous COVID-19 vaccine that has been on the market, voted this past week to manufacture new booster shots to target strains derived from the JN.1 variant, which include KP.2 and KP.3.

A survey released earlier this year said that one in five Americans believe COVID-19 is a “major threat” to the U.S. population, a sharp decline from a high of 67 percent in the summer of 2020.

What is FLiRT?

“FLiRT,” is a new family of COVID-19 variants and is now dominant in the United States.

The name comes from its mutation. It contains two new key mutations compared to the previous dominant variant JN.1. One mutation is “F456L,” representing an amino acid code change from “F” to “L” at the 456th amino acid of the spike protein chain. The other, “R346T,” represents the amino acid code change from “R” to “T” at position 346. These mutations are responsible for the behavior of the new variants.

Slightly More Infectious

According to a recent research preprint, the binding affinity of KP.2—which indicates how fast a new variant can infect people—increased by 1.2 times compared to that of the JN.1 variant.

Researchers used a binding affinity test that involves putting the angiotensin-converting enzyme 2 (ACE2) receptor (where the virus binds and invades the human cells) and variants into a system similar to a test tube. This type of test is fast, simple, and easy to control, while its weakness is that it does not represent the entire picture of what happens in the human body.

This data suggests a slightly higher infectivity rate for KP.2, which seems incompatible with the rate at which it is currently spreading. This indicates that there must be other reasons for the fast spread of the virus.

When assessing a variant’s infectivity and its ability to spread quickly in a population, there are many more proteins, molecules, and factors inside our human bodies that need to be considered.

‘Antibody’ Escape

While most media use the term “immune escape,” we would prefer to use the term “antibody escape’ because it is more accurate. Here is why.

When a virus invades our body, our immune system has various methods of fighting the invader. One of the most extensively researched ways is by producing antibodies.

Antibodies are protective proteins that our immune cells produce to clear viruses and other disease-causing foreign substances called antigens.

The preprint study suggests that neither a prior infection nor the latest booster based on the Omicron XBB variant, provide expected  protection against FLiRT.

Scientists studied five groups of people reinfected with COVID-19 by different combinations of Omicron variants. They tested the neutralizing ability of the antibodies in their blood with different variants. Three of the five groups had a history of vaccination.

The results showed a 1.5- to 1.9-fold reduction in the levels of neutralizing antibodies in response to FLiRT variants, compared with JN.1. This meant that people would not gain adequate protection against FLiRT from a previous COVID-19 infection or vaccination.

Other close relatives of FLiRT show a similar trend. Specifically, one subvariant called KP.3 was the strongest at escaping the immune system, with a 1.9- to 2.4-fold reduction in neutralizing antibodies, compared to JN.1.

Lock and Key

Since Omicron appeared, keeping up with the rate of constantly mutating variants has been difficult for the development of boosters.

Two major mutations in FLiRT, F456L and R346T, are located near the receptor-binding parts known to be related to antibody escape.

The interaction between the ACE2 receptor and the SARS-CoV-2 virus is like a key being inserted into a lock to gain entry into the cell. The virus mutants alter the shape of the parts of the “key” in contact with the receptor, making it easier to open the “lock.” This increase in binding affinity allows the virus to enter the cell and infect people more easily.

Meanwhile, the change in the key’s critical parts also impacts the antibody’s ability to bind and clear them. This is why vaccine efficacy could decrease.

Since the JN.1 era, the virus has gained additional tricks—including the “FLip” mutation (F456L + L455F) and non-spike protein mutations—to further weaken the antibody’s neutralization effects and escape from established immunity. As a descendant of the JN.1 family, FLiRT has inherited the same features.

Our Natural Immune Defense

Some people are worried about an upcoming summer wave linked to FLiRT, and others have suggested making another type of booster vaccine based on the new JN.1 variant.

This seems logical, as research has shown that natural and vaccine-induced immunity fades. However, changing the vaccine design may not be possible each time the virus changes its gene code.

Does our immunity to the virus simply depend on antibodies or do we have other effective ways to fight?

Our immunity isn’t lost when antibody escape occurs. It’s just one part of our immune system that’s weakened.

Our body has many powerful weapons against viruses, and antibodies are not the only tool we have. Children who cannot produce antibodies have demonstrated an ability to fully recover from viral infections like measles.

Our natural immunity can effectively fight a virus, regardless of how a variant mutates.

For example, when a virus invades the body, it triggers a defense mechanism involving interferon.

Interferon is a key antiviral protein that is secreted by the epithelial cells when a virus attaches. It activates an antiviral state, orchestrating pivotal downstream antiviral mechanisms.

Two recent articles published in Nature and Science have revealed that older adults produce fewer interferons, which explains why severe cases are most likely seen in this age group when infected with a virus.

The way we think can also impact our interferon production. People with a compassionate mindset have demonstrated a higher level of interferon. As we grow older, we often become more empathetic and considerate of others. The health benefits that come with these positive changes can potentially counteract the negative effects of aging.

Furthermore, recent scientific research has uncovered new immune defenses that were previously unknown.

Interferon triggers a range of specialized weapons to fight infections. One of these weapons, called guanylate-binding protein (GBP), operates as a vigilant guard against various invaders, including viruses and germs.

John MacMicking, a professor of microbial pathogenesis and immunobiology at Yale School of Medicine, recently described GBP1 as a “giant nanomachine” that could trap invading bacteria and viral intruders in our body.

When a germ enters the body, our immune cells release GBP1 proteins. These proteins act like sticky ropes and wrap around the germ, creating a net that traps it. Within a short period, the bacterium becomes surrounded by an inescapable straitjacket. As many as 30,000 GBP1 proteins can enclose the pathogen, effectively trapping it in a kind of body bag.

GBP1 plays a crucial role in antiviral defense against many viruses, including vesicular stomatitis virus, encephalomyocarditis virus, and dengue virus.

How many other powerful weapons does our body possess that we are not yet aware of?

Our miraculous innate ability to heal and fight off infections is a powerful tool we must not overlook. By focusing on safeguarding our natural immunity and healing power through a healthy lifestyle, we can reduce concerns about the FLiRT variant.

US FDA asks Covid-19 vaccine makers to instead target KP.2 strain for fall season

The FDA is directing Covid-19 vaccine manufacturers to update their formulations to target the KP.2 strain of the virus, citing higher circulation levels of that strain.

The agency’s Vaccines and Related Biological Products Advisory Committee previously recommended that manufacturers produce monovalent vaccines targeting the JN.1 strain of the virus. But based on disease activity in the US, the agency said on June 5th, 2024 that it determined that the strain instead should be KP.2.

“FDA has communicated this change to the manufacturers of the licensed and authorized Covid-19 vaccines,” the FDA said. “The agency does not anticipate that a change to KP.2 will delay the availability of the vaccines.”

A Pfizer spokesperson told Endpoints News that it’s having ongoing discussions with the FDA and global regulators about the composition of future Covid-19 vaccine formulations.

“We will continue to evaluate the data and will share further updates in due course,” the spokesperson said.

Novavax announced on June 14th, 2024 that it submitted its updated vaccine targeting the JN.1 lineage, which it says is active against multiple strains, including KP.2 and KP.3. The company said it will have doses for distribution by mid-July.

“Novavax is committed to having a protein-based Covid-19 option available at the start of the vaccination season, which is critical because research suggests that providing vaccine choice, along with healthcare provider recommendations, may help improve vaccination rates,” Novavax CEO John Jacobs said in a statement.

Moderna said in an emailed statement Friday that it plans to produce vaccines “in accordance with the latest regulatory guidance and strain recommendations from the FDA” in time for the fall vaccination season.

At last week’s VRBPAC meeting, committee members were concerned that Novavax, which manufactures protein-based vaccines, wouldn’t be able to produce a KP.2 vaccine in time for the fall season and thus were swayed toward choosing JN.1 to ensure a protein vaccine would be available. But FDA biologics center director Peter Marks pushed back during discussion, making his case to go with KP.2.

“I’m just a little concerned that perhaps the committee doesn’t understand that if they choose to recommend or to make any comments about a KP.2 vaccine that does not mean that … there will not be availability of a JN.1 Novavax vaccine,” Marks told the committee. “It just may mean that there will be two different formulations available.”

Next up, the CDC’s Advisory Committee on Immunization Practices is set to make a determination this summer about who should receive the updated vaccines. The CDC director will have to sign off on that decision before the vaccines can be rolled out in the fall.