This story was originally Originally published in WIRED Japan and translated from Japanese.
The Northern Hemisphere is entering a new wave of COVID-19 infections. While most countries around the world are acting as if the pandemic is over, the number of infections is surging again. The US Centers for Disease Control and Prevention (CDC) has recorded an increase in COVID-19 positive tests, emergency department visits, hospitalizations and deaths in recent weeks, and the UK is also seeing a gradual increase in the number of infections and hospitalizations.
However, the surge in cases is particularly notable in Japan. The National Institute of Infectious Diseases has reported a sharp increase in the number of cases per medical institution since June. Okinawa Prefecture in particular has recorded the highest number of newly hospitalized patients since reports began, and the spread of infection in the country could surpass the two previous major outbreaks in September 2023 and January 2024.
The surge in infections is due to new variants KP.3, LB.1, and KP.2.3. Descendants of the Omicron sublineage JN.1 that became dominant at Christmas, KP.3 appears to be the driving force behind new infections around the world. As of July 15, the US CDC estimates that about 37% of new US COVID-19 cases are due to KP.3, 24% are due to KP.2, and 15% are due to LB.1. KP.3 has been increasing rapidly over the past few months, accounting for about 9% of US cases as of May 11, but 25% a month later on June 11.
These viruses are collectively known as FLiRT mutants because of mutations in the spike protein that change the 456th amino acid from phenylalanine (F) to leucine (L) and the 346th amino acid from arginine (R) to threonine (T). According to a paper from the Institute of Medical Science at the University of Tokyo published in The Lancet Infectious Diseases earlier this year, these mutants are more transmissible and have a greater ability to evade neutralizing antibodies than previous mainstream mutants.
Genotype to Phenotype Japan (G2P-Japan), a research consortium from the institute, estimates that the R numbers (average number of new infections per infected person, an indicator of infectivity) of FLiRT variants are higher for these new types of viruses than JN.1. Furthermore, when the infectivity of these viruses was assessed in cultured cells, KP.3 required smaller amounts of virus to cause infection, while both LB.1 and KP.2.3 required roughly the same amount of virus as JN.1. These results provide clues as to why KP.3 appears to be moving towards dominance.
FLiRT variants, including KP.3, are also better able to evade immunity than previous viruses. When the G2P-Japan team looked at responses to neutralizing antibodies elicited by past infections, breakthrough infections (infections that occur after vaccination), and the improved XBB.1.5 Covid vaccine, they found that in all cases neutralizing activity against FLiRT was significantly weaker than against existing circulating variants.
