‘FLiRT’ COVID-19 subvariant dominant in Canada. What to know about the strain

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Canada’s lull in COVID-19 cases faces a potential disruption with the emergence of a new family of subvariants, playfully dubbed the ‘FLiRT’ variants.

These genetic cousins, originating from JN.1, the Omicron subvariant that fuelled the winter surge, are now spreading nationwide, with one variant, KP.2, quickly gaining dominance in Canada.

KP.2 is the dominant subvariant of the JN.1 strain, explained Gerald Evans, an infectious disease specialist at Queen’s University in Kingston, Ont. As of April 28, national data shows that KP.2 accounted for 26.6 per cent of all COVID-19 cases in Canada, surpassing other JN.1 subvariants.

“The nomenclature KP.2. really throws people for a loop,” Evans told Global News. “But it’s just a continued evolution of what we’ve been seeing for the last bit of time since the beginning of this year, which is the JN.1 lineage.”

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This subvariant, as well as KP.1 and KP.3, make up what is known as the FLiRT variants, Evans said.

“FLiRT is a bit of an odd name, and it’s not like one of these names that’s been given by a social media person,” he said, adding there is scientific meaning behind it.

They are nicknamed FLiRT mutations because the amino phenylalanine (abbreviated as F) replaces the amino acid leucine (abbreviated as L), while the amino acid arginine (R) is replaced by threonine (T), he said.

“And the I is just in there to make it sound like a real word. So that’s what FLiRT stands for. It’s just a designation to talk about where the mutations line,” he said.

What is KP.2?

On Wednesday, the World Health Organization (WHO) stated that the KP.2 subvariant began circulating globally in January.

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“KP.2 is a descendant lineage of JN.1, which is the dominant strain worldwide,” Maria Van Kerkhove, WHO’s technical lead for COVID-19, said during a Wednesday virtual press conference. “KP.2… has additional mutations in the spike protein. There are other emerging variants, and JN.1 continues to evolve we will continue to see these variants circulating.”

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She added that the WHO continues closely monitoring the virus’s evolution.

In Canada, the emergence of KP.2 was first observed in February. Evans clarified that it’s named “KP.2” because when a variant accumulates more than three numbers in its designation, a new prefix is assigned. In this case, JN.1 turned into KP.2

“It’s because of this funny prefix change that people think, ‘Oh, it’s a whole new variant’,” he said. “It’s just the continued evolution of the viruses.”

Is KP.2 more contagious?

While COVID-19 levels are currently relatively low on average across Canada, Dr. Isaac Bogoch, an infectious diseases specialist, highlighted the latest mutation suggests it may be more adept at evading our immunity, potentially indicating a looming spike in COVID-19 cases.

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“This year we didn’t see much of a spring COVID-19 wave,” Bogoch told Global News. “Could [KP.2] cause an uptick of COVID infections? Sure it could. The mutations might enable the virus to circumvent current immunity and cause reinfection. But typically, on average, the severity of those infections is lower.”

Bogoch said although the FLiRT variants may be able to better evade people’s immunity, we are “still not dealing with an immuno-naive population.”

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He emphasized that the majority of individuals have either been infected with COVID-19, vaccinated, or both. This implies that the virus poses less of a threat to healthy adults and children. However, he underscored that it remains a significant concern for seniors and immunocompromised individuals.

“People of course can still get infected and reinfected. But the severity of illness is on average much less,” he said.

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Evans agreed, noting that although current data indicates the KP.2 subvariant possesses a reproductive advantage, it still has a notably diminished growth rate compared to previous variants.

“It looks like it’s not quite as infectious as the previous generations,” Evans said. “And the most preliminary data from experiments in research labs shows that it’s about a tenfold diminishment in its infectivity. So that’s great because it means it’s less infectious and less likely to potentially infect someone if you come in contact with it to some degree.”

FLiRT COVID symptoms: What are they?

While acknowledging that the data is still fresh, Bogoch noted that so far, symptoms of the FLiRT variants appear to align closely with those of all Omicron ones.

“We know what the symptoms typically are for COVID-19. It’s unlikely that there’ll be any surprises on that front,” he said.

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Symptoms of COVID-19 include:

  • sore throat
  • runny nose
  • sneezing
  • new or worsening cough
  • shortness of breath or difficulty breathing
  • feeling feverish
  • chills
  • fatigue or weakness
  • muscle or body aches
  • new loss of smell or taste
  • headache

Does the current vaccine work against FLiRT variants?

The COVID-19 vaccine currently accessible in Canada targets the XBB 1.5 Omicron subvariant. Evans clarified that despite its lack of inclusion of the JN.1 virus, it is expected to provide efficacy against the FLiRT variants.

“It is offering some protection against the JN.1,” he said.

Evans emphasized that if you’re young, and in good health, having received your COVID-19 vaccine in the autumn, another booster likely won’t be necessary until fall 2024.

However, for Canadians aged 65 and above, as well as those who are immunocompromised, he advised getting the spring booster.

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Last week, the National Advisory Committee on Immunization (NACI) released its fall 2024 COVID-19 vaccine guidelines, saying it anticipates another surge in the fall and winter months.

“An updated vaccine to replace the current XBB.1.5 vaccine may be available starting in the fall of 2024, depending on the epidemiology of SARS-CoV-2 and recommendations of international advisory groups expected in mid-spring 2024,” NACI noted.

On Wednesday, the WHO said its Technical Advisory Group on COVID-19 Vaccine Composition recommended that future formulations of the shot include JN.1.

“The WHO is deciding on using JN.1 for vaccine manufacturing as the template and we’ll hear from the United States probably next month.,” Bogoch said.

“But if it’s an arms race and we’re trying to stay ahead of the virus, it’s going to be extremely difficult because the virus is going to continue to mutate, very similar to playing catch-up with influenza vaccines and a constantly changing influenza virus.”


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