CNA Explains: The FLiRT family of COVID-19 variants and what we know about the KP.2 strain

SINGAPORE: Another COVID-19 wave has hit Singapore, with the KP.1 and KP.2 variants accounting for more than two-thirds of cases here.

The two strains belong to a new family of subvariants called “FLiRT”, which is also spreading elsewhere in the world. 

Here's what we know about the new variants.

WHAT ARE THE KP.1 AND KP.2 STRAINS?

KP.1 and KP.2 belong to a group of COVID-19 variants scientists have nicknamed “FLiRT”, after the technical names of their mutations.

The strains in FLiRT are all descendants of the JN.1 variant, an offshoot of the Omicron variant. The JN.1 variant spread rapidly around the world several months back and was responsible for Singapore's COVID-19 wave last December. 

The KP.2 strain, in particular, appears to be spreading faster than KP.1.

In May, KP.2 was classified by the World Health Organization as a Variant Under Monitoring. This signals to public health authorities that a COVID-19 variant may require prioritised attention and monitoring.

KP.2 was first detected in India in early January.

It has since become the dominant strain in the United States, accounting for about 28 per cent of infections in the country in mid-May. This is up from just 6 per cent in mid-April and 1 per cent in mid-March, according to data by the US Centers for Disease Control and Prevention (CDC).

KP.2 has also spread to other countries, including China, Thailand, Australia, New Zealand and the United Kingdom.

ARE THE NEW STRAINS MORE INFECTIOUS?

The US CDC said on May 16 that while KP.2 is the main variant, it isn’t causing more severe illness than other variants.

Singapore's Health Ministry similarly said on May 18 that there are currently no indications that KP.1 and KP.2 are more transmissible or cause more severe disease than other circulating variants.

But slight differences in KP.2’s spike protein might make it better at evading our immune defences and slightly more infectious than JN.1, according to Dr David Ho, a virologist at Columbia University who was quoted by the New York Times.

It could even infect people who received the most updated vaccine, Dr Ho added, since that shot targets XBB.1.5, a variant that is different from JN.1.

"They certainly can evade the immunity conferred by the earlier vaccinations ... or earlier infections before JN.1," said Dr Leong Hoe Nam, an infectious diseases expert at Rophi Clinic in Singapore.

He was referring to earlier versions of COVID-19 vaccines such as the bivalent ones.

DO KP.1 AND KP.2 CAUSE MORE SEVERE SYMPTOMS?

The symptoms for KP.1 and KP.2 are the same as earlier variants, Dr Leong said, adding that there is no indication the variants lead to more severe illness.

In fact, said Professor Paul Tambyah who cited the Infectious Diseases Society of America, disease caused by KP.2 and KP.1 is less severe than their ancestor JN.1. 

However, KP.2 and KP.1 may be more transmissible, said Prof Tambyah, who is the president of the International Society for Infectious Diseases. Their behaviour follows that of all viruses, which eventually evolve to become more transmissible and less virulent.

"Even the deadly 1918 influenza pandemic virus, which killed one in 50 people worldwide, simply evolved to become the dominant strain of seasonal influenza from 1920 to 1957," noted Prof Tambyah.

Like JN.1 and previous Omicron variants, it may take five or more days before a person starts to develop symptoms after exposure, although symptoms may appear sooner, said Professor Andy Pekosz from the John Hopkins Bloomberg School of Public Health.

“When it comes to symptoms, we’re not seeing anything new or different with these variants,” he added.

“We continue to see more mild disease, but that’s likely not because the virus is milder, but because our immunity is so much stronger now.”

Symptoms include fever, sore throat, runny nose and fatigue.

Fewer people lose their sense of taste and smell now than they did at the start of the pandemic, but some may still experience those symptoms.

Infected people could also experience gastrointestinal symptoms like diarrhoea, nausea and vomiting, which are sometimes confused with norovirus symptoms.

SHOULD WE BE WORRIED ABOUT KP.1 AND KP.2?

Globally there has not been a large number of hospitalisations. The mortality rate has also remained low. 

Dr Leong said that there will be a “minor uptick” in cases in Singapore over the next few weeks due to the KP.1 and KP.2 variants.

He added, however, that this increase will be “relatively minor compared to JN.1", as prior infection from JN.1 will confer “significant protective benefit” to KP.1 and KP.2.

Immunity from previous and ongoing vaccinations, previous infection and personal hygiene measures might reduce the height of this surge, said Dr Shawn Vasoo, clinical director of Singapore's National Centre for Infectious Diseases.

"We’ve been through multiple waves of COVID-19. Right now, there is no increased concern about these new strains compared to previous Omicron variants," he added.

The danger is that repeat infections could raise the risk of developing long-COVID, said Dr Fikadu Tafesse, a virologist at Oregon Health & Science University.

And there is no cure for long-COVID, Dr Leong noted. "It is a black hole of unknowns," he said, adding that people should get vaccinated to avoid the risk of long-term illness.

According to Dr Tambyah, MOH data suggests that COVID-19 numbers are already plateauing. "Things might change with the school holiday travel but I doubt it would change much," he said.

ARE CURRENT VACCINES STILL EFFECTIVE?

Against JN.1, the current vaccines designed around Omicron XBB.1.5 do generate some cross-reactive antibodies, said Professor Pekosz.

Studies have not been done with some of the newer variants, he noted, adding that those are likely to be "a little less cross-reactive".

Dr Leong provided a similar view. 

“We know that the XBB1.5 vaccine was about 50 per cent effective against the JN.1. We suspect that the current vaccine will be less effective in preventing infections with KP.1 and KP.2,” he told CNA.

"The chief reason is the presence of the FLiRT mutations. The F amino acid became L and the R became a T. This allowed the virus to evade the existing immunity against COVID."

It has also been several months since many people received their last dose of the vaccine, and that immunity wanes over time.

Scientists say vaccination remains the best bet, especially against severe illness.

“We firmly believe that it (the vaccine) is still effective against preventing severe disease such as hospitalisation and death,” Dr Leong said.

Singapore's Health Ministry said that during the peak month of the previous JN.1 wave in December 2023, the incidence rate of COVID-19 hospitalisations and intensive care admissions among seniors aged 60 and above was 25 per cent higher in those who had not kept their vaccination updated compared to those who had.

The US CDC said the agency was continuing to monitor how vaccines perform against KP.2.

Governing bodies like the WHO and the US Food and Drug Administration are also expected to recommend a formulation for updated COVID-19 vaccines that will roll out in early fall.

New COVID-19 variants are likely to crop up after a decision is made, but Professor Pekosz said the goal remains to select a formulation that will match the circulating variants as closely as possible.

ARE TEST KITS STILL EFFECTIVE?

Dr Leong and Dr Vasoo said COVID-19 test kits are able to detect the KP.1 and KP.2 variants.

"The COVID-19 test kit tests against the N protein. But the mutation of KP variants is mainly due to the spike protein," Dr Leong explained.

"In fact, the N protein has been consistently stable with only minor mutations since the beginning."

Dr Vasoo noted that some lateral flow tests have been reported to have possibly diminished performance with the Omicron variants.

"However, they can still detect the KP.1 and KP.2 variants," he said.

Testing gives a definite diagnosis, which can better guide a treatment plan as many COVID-19 symptoms overlap with that of other respiratory viruses such as influenza.

"This is more pertinent for the medically vulnerable or elderly, who require closer monitoring of their symptoms to prevent worsening of their condition or specific medical treatment," Dr Vasoo advised.