Mutated H1N1 Flu Drives an Early US Season, With January Levels Already in Washington

Flu season has started months ahead of schedule in the United States, and it started in the wrong place. Dr. Alex Greninger, who heads infectious disease diagnostics at the University of Washington in Seattle, said this year's season began about two and a half months earlier than usual and hit West Coast states first. In a typical year, the season starts in the South, often in Florida, and spreads north as fall and winter progress.

January levels in October

About 1 in 10 people tested for flu in Washington state last week tested positive, according to state health department data cited by CNN. "We are basically seeing January levels of flu in the last week," Greninger said. Seattle usually peaks in January, with most cases arriving from late December through February.

Walgreens says this season is tracking about four weeks ahead of recent seasons nationally, with more antiviral prescriptions than at the same point last year. Nationally, about 2.1 percent of doctor visits last week were for influenza-like illness, according to the US Centers for Disease Control and Prevention. That is still below the national baseline, so the virus has not taken off everywhere.

Dr. Caitlin Rivers, an epidemiologist at Johns Hopkins University, said the Pacific states all started very early and activity is now spreading east, with increases in every region. In the region covering Arizona, California, Hawaii and Nevada, at least 10 percent of flu tests came back positive last week, and the South is catching up quickly, she said.

The mutated strain

The early wave is dominated by H1N1, the flu virus that caused a pandemic when it first emerged in 2009. Greninger said H1N1 accounts for about 98 percent of the samples reaching his laboratory. In US data for the week ending Sep 26, H1N1 made up 96 percent of positive cases for which subtyping was done, Nature reported.

Many of these viruses carry a mutation called G155E that helps them evade existing immunity. Nature reported on Oct 6, 2026 that the mutation showed up in 13 of 17 Seattle H1N1 samples that could be fully sequenced. Research led by Jesse Bloom at the Fred Hutchinson Cancer Center found that antibodies from many people, especially teenagers and young adults, were less able to recognize strains with this mutation.

The mutation appeared after the strains for this year's flu shots had already been chosen in the spring. The shots still target H1N1 and should still offer some protection, Greninger said, but the changed virus can break through. In Japan, this version of the virus forced school and day care closures after cases surged among children, and officials moved vaccination clinics earlier.

Get vaccinated now, doctors say

Doctors often advise getting a flu shot before Halloween so protection lasts through spring. Greninger said the right time this year was two to three weeks ago, and that people who have not had the shot should get one as soon as possible. Rivers said she worries about vaccine timing, because people are not thinking about flu shots this early in the season.

Most US flu shots are still grown in chicken eggs, which is why strains must be picked months ahead. A newly approved mRNA flu shot could let makers produce better matched vaccines faster, Greninger said.

Whether the early start makes the whole season worse is not yet known. Greninger said a second wave could follow after H1N1 peaks, with more flu possible in January, February or March.