Q&A: What to know about the SARS-CoV-2 ‘FLiRT’ variants – Healio

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Together, a group of viruses nicknamed FLiRT have emerged to become the most common SARS-CoV-2 variants in the country.

According to the CDC, in the most recent week with available data, there was a 1.2% increase in SARS-CoV-2 test positivity in the United States, a 14.7% increase in ED visits related to COVID-19 and a 16.7% increase in COVID-19 linked deaths, and COVID-19 hospitalizations increased by 25% during the last week of May.

We asked Bruce Y. Lee, MD, MBA, professor of health policy and management at the City University of New York School of Public Health, about the new variants and the potential for a summer surge in COVID-19 cases.

Healio: What are the FLiRT variants of SARS-CoV-2?

Lee: FLiRT refers to a new group of SARS-CoV-2 omicron variants that have two mutations in their spike proteins. The name comes from the amino acid changes that comprise these mutations: a change of phenylalanine (F) for leucine (L) at position 456 and arginine (R) for threonine (T) at position 346.

These variants are descendants of the JN.1 variant that was dominant in the United States earlier this year and includes various variants whose names begin with the letters JN and KP that are now spreading in the U.S.

In the first week of June, KP.3 accounted for an estimated 33.1% of SARS-CoV-2 infections in the U.S., KP.2 for an estimated 20.8% and KP.1.1 for an estimated 9%.

Healio: Is there anything that worries you about these variants more than other SARS-CoV-2 variants?

Lee: These FLiRT variants appear to be rapidly spreading throughout the U.S. Preliminary data suggest that the Re the effective reproduction number for KP.2 may be 1.22 times higher than the Re for JN.1.

The mutations are in locations of the spike protein where antibodies against the virus typically bind. The big question is whether these will make antibodies less likely to bind to the virus spike protein and thus decrease the protection offered by vaccination or previous SARS-CoV-2 infections. So far, it looks like vaccination remains effective against the FLiRT variants, but more data are needed.

Healio: Is there really a summer surge in COVID-19 cases right now?

Lee: This is difficult to tell since many COVID-19 cases are probably going undiagnosed because many people may not be getting tested when they have been exposed or are experiencing symptoms, unlike earlier in the pandemic.

Many COVID-19 cases are also probably going unreported because many people may not be telling others such as public health authorities when they have tested positive for COVID-19.

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Q&A: What to know about the SARS-CoV-2 'FLiRT' variants - Healio