FDA modifies strain recommendation for fall COVID vaccine amid variant shifts, uptick in cases

Though the US Food and Drug Administration (FDA) last week recommended that vaccine companies switch to the JN.1 variant for updated shots for the fall, yesterday it urged companies to focus on the KP.2 lineage if possible, based on recent shifts and a national rise in cases.

On June 5, the FDA’s vaccine advisory group recommended a switch to the JN.1 variant, though it held off on recommending the KP.2 offshoot of JN.1, partly due to uncertainties about further evolution of SARS-CoV-2 strains. The group was also concerned about the availability of Novavax, which as a protein-based vaccine that has a longer production timeline and would not be able to switch to the more specific KP.2 lineage.

Shortly after, the FDA accepted the advisers’ advice but said it would continue to monitor the safety and efficacy of COVID-19 vaccines, along with the evolution of the virus. In its latest variant proportion update, the Centers for Disease Control and Prevention (CDC) reported another jump in KP.3 proportions, along with a further rise in KP.2 viruses and a steady decline in the JN.1 parent lineage.

A closer match for circulating strains

The two rising offshoots have the mutations that are thought to make them more evasive to immunity from earlier infection or previous vaccination.  

In its statement yesterday, the FDA said that, based on the latest data, including rises in COVID-19 activity in some parts of the country, the preferred vaccine lineage is KP.2, and that a switch from the original JN.1 recommendation is intended to ensure that 2024-25 COVID vaccines more closely match circulating strains.

“The agency does not anticipate that a change to KP.2 will delay the availability of the vaccines for the United States,” the FDA said. mRNA vaccines have a shorter production timeline and appear well poised to incorporate the change.

Novavax, which produces the protein-based option, said its vaccine provides broad cross-neutralization against a range of JN.1 descendant viruses, including KP.2 and KP.3. It also said the vaccine produces conserved T-cell responses against a range of JN.1 offshoots. 

“These responses indicate that our vaccine technology induces broadly neutralizing responses against multiple variant strains, including to circulating forward drift variants,” it said in a statement, which was first posted on June 5, then updated on June 10.

The company said it expects to have the vaccine ready for commercial delivery in September, pending FDA authorization.

Hawaii is a US hot spot

In its data updates today, the CDC reported more rises in its early COVID indicators, which have shown a small uptick over the past few weeks from very low levels. The percentage of tests with positive results rose slightly and is highest in the western region that includes Arizona, California, Hawaii, and Nevada.

Emergency department visits from COVID were up modestly. Hawaii has the highest level, which is listed as moderate. Other states are at the minimal level or don’t have enough data for analysis. 

Earlier this week, the Hawaii State Department of Health urged the public to be vigilant because of high COVID levels, which are at the red level, meaning they are at high levels compared to historic trends. “This high level means that recommended precautions are more important for reducing risk,” it said.

In a respiratory virus illness snapshot today, the CDC estimated that COVID levels are growing or likely growing in 34 states or territories, declining in 1, with the trend uncertain in 14. “An increasing proportion of the variants that cause COVID-19 are projected to be KP.3 and LB.1,” the agency said. LB.1 is another JN.1 offshoot showing rising proportions.

Hawaii’s health department urged people to be up to date with their recommended vaccine doses, especially seniors, to stay home when sick and take extra precautions in the household, to wear a well-fitted mask indoors with other people, and to test if having symptoms.

CDC wastewater tracking show that overall levels are low, but up sharply in the West. Meanwhile, the latest data from WastewaterSCAN, a national wastewater monitoring system based at Stanford University in partnership with Emory University, suggest that COVID levels are in the high category nationally and in the South and Northeast, with concentrations medium and on an upward trend over the past 3 weeks. It put the Midwest and the West in the medium category.