Based on adult deaths from flu and pneumonia, this season is the worst since 2003-2004 -- another time when the vaccine did not include the exact flu strain responsible for most illnesses.
Each year, health officials -- making essentially an educated guess -- formulate a vaccine against three viruses they think will be circulating. They guess well most of the time, and the vaccine is often between 70 and 90 percent effective.
But this year, two of the three strains were not good matches and the vaccine was only 44 percent effective, according to a study done in Marshfield, Wis.
The CDC compares flu season by looking at adult deaths from the flu or pneumonia in 122 cities. This year, those deaths peaked at 9 percent of all reported deaths in early March, and remained above an epidemic threshold for 13 consecutive weeks. In 2003-2004, they peaked at more than 10 percent of all deaths, and surpassed the epidemic threshold for nine weeks.
"Our season is not quite as high but is lasting a little longer," said Dr. Dan Jernigan, deputy director of the CDC's influenza division.
Pediatric deaths are another way flu seasons are compared. So far this year, 66 children died, including 46 who were not vaccinated. In 2003-2004, 153 children died.
The CDC started working this year with the Marshfield Clinic in central Wisconsin to get a better gauge of vaccine effectiveness while a flu season was in progress. Almost the entire population gets health care at the clinic, which has complete vaccination and electronic medical records.
This year, a Type A H3N2 Brisbane strain not in the vaccine has been responsible for most of the illnesses. A Type B Florida strain, also absent from the vaccine, has also been causing illness. Marshfield data showed that the vaccine didn't work at all against the Type B virus, and was 58 percent effective against the Brisbane virus.
Jernigan acknowledged that some people may lose faith in the flu vaccine and skip it next year. But he noted even this year, when the vaccine was not a good match, the vaccine still offered 44 percent protection overall.
The Marshfield study and a flu season update are being published this week in a CDC publication, Morbidity and Mortality Weekly Report.