The flu virus is rampaging across New England, spawning waves of coughs and fevers, causing patients to flood doctors' offices, and raising questions about the effectiveness of flu shots given to tens of millions of Americans.
During the past two winters, the influenza season proved unusually mild in New England and much of the nation. But this year is strikingly different, with federal disease specialists reporting yesterday that virtually every state now has widespread flu activity.
"We're seeing it raging," said Dr. Alfred DeMaria, the top disease tracker in Massachusetts.
At Massachusetts General Hospital's network of clinics and hospital wards, the number of patients testing positive for influenza so far this season is already 21 percent higher than for all of last winter.
At Harvard Vanguard Medical Associates, doctors report that their patients must sometimes wait an hour for care because so many people are showing up with flu symptoms.
And at Boston's Health Department, the tally of laboratory-confirmed flu cases last week reached its highest level since the city started intensively tracking lab results four or five years ago.
While specialists can't say for sure why this year is so much worse, they know this much: The strains of flu virus used to make this season's vaccine aren't a good match with what's circulating, meaning that the shot provides a weaker shield of protection than in most years.
The evidence of that can be found in the Jamaica Plain offices of the Massachusetts Department of Public Health.
"Everybody here gets vaccinated, so the fact that we've had significant absenteeism in our own organization suggests to me the vaccine has not been as effective as we would have hoped," DeMaria said.
When federal authorities tested flu samples collected from US patients in recent weeks, they found that more than half contained strains not covered by the vaccine.
"It's certainly not a perfect vaccine, even in the best years," said Dr. Joe Bresee, a flu specialist at the US Centers for Disease Control and Prevention.
That's because making flu vaccine is an archaic process using chicken eggs, which forces specialists to pick the formula for each year's shots eight months before the next season starts in the United States.
Federal specialists are meeting Thursday to decide the ingredients for the 2008-2009 flu vaccine.
The vaccine recipe is determined by studying which strains of the virus are prevalent elsewhere in the world and expected to migrate to the United States. This year, two strains specialists didn't predict would be troublesome have become prime culprits.
"The timing makes it very complicated," said Dr. David Hooper, chief of the infection control unit at Mass. General. "They certainly do their best to estimate the strain most likely to be circulating. But, ultimately, it's nature's call."
The genetic content of the germ is constantly and subtly changing in response to the immunologic defenses it encounters in its victims. So by the time the flu virus lands in the United States, its genetic structure can have adapted just enough to elude the vaccine.
Specialists said they fear that patients may be less inclined to be vaccinated in the future because this year's shot failed to work as well as hoped.
"I'm very concerned," said Dr. Timothy Ferris, medical director of the Mass. General Physicians Organization. "We have dramatically increased our use of the flu vaccine. We were sort of on a roll and felt like we were really making a lot of headway."
To be sure, though, the mismatch between the vaccine and this year's strains can't fully explain the current bounty of flu cases.
Many of the patients falling ill had not been vaccinated, doctors lamented, adding that even a less-than-perfect vaccine can provide some protection and lessen the severity among people who become ill.
Dr. Benjamin Kruskal, director of infection control for Harvard Vanguard, said his system has been so busy in recent weeks that some practices were forced to double-book patients just to keep up with the demand.
If patients are able to get to the doctor within a day or two of the start of symptoms, they can get prescriptions for drugs such as Tamiflu that can shorten the duration of their misery.
Otherwise, there is little doctors can do.
On Wednesday, Mass. General's Ferris became a patient himself.
"I've been around a ton of flu in the past couple of weeks given my job," said Ferris, who always gets a flu shot.
He was at a meeting Wednesday evening when chills and aches descended.
By yesterday morning, his wife had sequestered him in the guest room of their Cambridge home in hope that he would not spread the virus to her or their three children.
Asked to describe how he was feeling, he responded, through sniffles, "I can't actually use the word in polite company."
Stephen Smith can be reached at stsmith@globe.com.
