As COVID cases rise again, what do I need to know about the new FLiRT variants?

We’ve now been living with COVID for well over four years. Although there’s still much to learn about SARS-CoV-2 (the virus that causes COVID) at least one thing seems clear: it’s here to stay.

From the original Wuhan variant, to Delta, to Omicron, and several others in between, the virus has continued to evolve.

New variants have driven repeated waves of infection and challenged doctors and scientists seeking to understand this changing virus’ behaviour.

Now, we are faced with a new group of variants, the so-called “FLiRT” variants, which appear to be contributing to a rising wave of COVID infections around Australia and elsewhere. So where have they come from, and are they cause for concern?

A descendant of Omicron

The FLiRT variants are a group of subvariants of JN.1 from the Omicron lineage.

JN.1 was detected in August 2023 and declared a variant of interest by the World Health Organization in December 2023. By early 2024, it had become the most dominant variant in Australia and much of the rest of the world, driving large waves of infections.

As new variants emerge, scientists work hard to try to understand their potential impact. This includes sequencing their genes and assessing their potential to transmit, infect and cause disease.

In late 2023 scientists detected a range of subvariants of JN.1 in wastewater in the United States. Since then, these JN.1 subvariants, including KP.1.1, KP.2 and KP.3, have popped up and become more common around the world.

But why the name FLiRT? Sequencing of these subvariants revealed a number of new mutations in the virus’ spike protein, including F456L, V1104L and R346T. The name FLiRT was coined by combining the letters in these mutations.

The spike protein is a crucial protein on the surface of SARS-CoV-2 that gives the virus its spiky shape and which it uses to attach to our cells. Amino acids are the basic building blocks that combine together to form proteins and the spike protein is 1,273 amino acids long.

The numbers refer to the location of the mutations in the spike protein, while the letters designate the amino acid mutation. So for example, F456L denotes a change from F (an amino acid called phenylalanine) to L (the amino acid leucine) at position 456.

What do we know about FLiRT’s characteristics?

The regions of the spike protein where the mutations have been found are important for two main reasons. The first is antibody binding, which influences the degree to which the immune system can recognise and neutralise the virus. The second is virus binding to host cells, which is required to cause infection.

These factors explain why some experts have suggested the FLiRT subvariants may be more transmissible than earlier COVID variants.

There are also very early suggestions the FLiRT subvariants could evade immunity from prior infections and vaccination better than the parental JN.1 variant. However, this research is yet to be peer-reviewed (independently verified by other researchers).

In more positive news, there’s no evidence the FLiRT variants cause more severe disease than earlier variants. Still, that doesn’t mean catching a COVID infection driven by FLiRT is risk-free.

Overall though, it’s very early days in terms of published research on these new FLiRT subvariants. We will need peer-reviewed data to understand more about FLiRT’s characteristics.

The rise of FLiRT

In the US, FLiRT has overtaken the original JN.1 variant as the dominant strain. The latest data from the US suggests the original JN.1 is making up less than 16% of cases.

While the FLiRT subvariants were detected in Australia more recently, they appear to be gaining traction. For example, NSW Health data up to mid May showed the proportion of KP.2 and KP.3 samples was continuing to increase.