Summer 2024 Covid-19 Surge Occurring With FLiRT Variants Taking Over

You could say that the U.S. is more than flirting with yet another Covid-19 surge. Chances are that a surge has already been occurring for at least a month—since early June. And the “FLiRT” variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been front-and-center of this surge.

Now, the U.S. still doesn’t have a comprehensive surveillance system that can catch surges before they happen or soon after they start happening even though it’s been over four and a half years since the the SARS-CoV-2 first surged in the U.S. Plus, nowadays, you don’t see the public health alerts about Covid-19 surges that you saw during the first three years of the pandemic. So, these days if you want to know whether Covid-19 is surging, you have to rely on checking Covid-19-related emergency room visits, hospitalizations and deaths to see if a surge has already been occurring with an emphasis on the words “has already been.”

Indeed, emergency room visits due to Covid-19 from June 16 through June 22—that’s two weeks ago—were up 23.3% from the previous week, according to data posted on the Centers for Disease and Control and Prevention. Also, Covid-19-related hospitalizations during the week of June 9 through 15 were 13.3% higher than they were than the week before. Recall that it can take a week or two after someone gets infected to develop symptoms severe enough to require an emergency room visit or a hospitalization. All of this suggests that Covid-19 cases were rising throughout most of June.

It shouldn’t be too surprising that yet another Covid-19 Summer surge has been happening. Many political and business leaders are not advocating for Covid-19 precautions such as face mask use and indoor air filtration and purification. And take a wild guess as to what may happen to a virus that’s still spreading and mutating when you don’t really do much to prevent its spread. The answer is not that it will go away on its own. Moreover, it’s been about 10 months since the last Covid-19 vaccine update was rolled out last fall, and protection offered by the vaccine tends to wane significantly after four to six months.

Then there are the “FLiRT” variants, a new group of SARS-CoV-2 omicron variants that have two key mutations in their spike proteins. If you recall, the spike proteins are what makes the virus looks like a spiky ball and help the virus latch on to your cells to then invade them. The name FLiRT is derived from the actual amino acid changes that result from the pair of mutations: a switch of a phenylalanine (F) for a leucine (L) at position 456 and arginine (R) for threonine (T) at position 346 in the spike protein.

These FLiRTs are descendants of the JN.1 variant that was dominant in the United States earlier this year and encompass a group of variants with names that begin with the letters JN and KP. 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%. And these percentages have been growing, which is not surprising since preliminary data has suggested that the R_e—the effective reproduction number—for KP.2 may be 1.22 times higher than the R_e for JN.1.

Whenever new variants emerge, the big question is whether they will be able to evade the existing protection that you may have from vaccination or previous Covid-19 infections. Well, the two mutations in the FLiRT variants do affect important locations in the spike protein—namely where antibodies against the virus typically bind. Nevertheless, so far, there’s no indication that vaccination will not be effective against the FLiRT variants. But—and this is big “but,” one cannot lie—more data are needed to determine how effective vaccination will be against the FLiRT variants.

Covid-19 is less of a concern now than it was in the earlier days of the pandemic. Your immune system is probably more used to the spike protein and the virus now. You are likely less likely to get hospitalized and suffer more severe consequences when infected with SARS-CoV-2. But the risks of more severe outcomes are still there. There is still a significant chance of suffering long Covid. Therefore, it is a good idea to maintain appropriate precautions such as making sure that indoor locations are well-ventilated and wearing a face mask when you may come into close sustained contact with others who may be infected. And a summer surge does increase the latter possibility.