It’s been almost a year since the first diagnosed case of swine flu in San Francisco and six months since President Obama declared the pandemic a national emergency.

Last October, the city’s public health department administered 20,000 vaccines in a three-day period. Then, one day in January, close to 14,000 people. To date, public officials said that about 400,000 San Franciscans have been vaccinated – that’s almost half the city.

That has helped avoid the pandemic that the government warned might cause up to 90,000 deaths in the United States. The virus only brought 12,000 – 546 in California – and the numbers have dwindled. In San Francisco – where only eight people have died of swine flu – providers say the mad rush to vaccinate has also slowed.

But Dr. Charles Chiu, an infectious disease expert at UCSF, said people shouldn’t be so quick to dismiss the swine flu as last season’s virus.

The flu could pick up again in the late spring or early summer, he said. It likes the opposite kind of weather that the seasonal flu — the trusted cold-weather virus – flourished in.

But why worry? While the seasonal flu killed about 36,000 Americans a year, the swine flu only killed 12,000 in its one-year run. And swine flu has virtually replaced the seasonal flu – about 99 percent of flu cases are swine flu cases. The new pandemic actually saved lives, according to the numbers.

But Dr. Chiu said while fatalities were down, the numbers don’t take into account the age group of those who died of swine flu – mostly the young or the pregnant. With the seasonal flu, 90 percent of the deaths were in people 65 and older, but 88 percent of the swine flu deaths took people under 65.

“It does cause fewer deaths but if you actually look at it from the point of view of years of life lost, this flu is actually worse,” said Chiu.

He said the elderly are largely immune to the virus because they’ve got the 1918 flu virus in their systems, which stayed in the air for decades after the fact. That flu – the Spanish Influenza – killed up to 40 million people worldwide and 600,000 Americans and the majority were healthy young adults.

The director of the Viral Diagnostics and Discovery Center in China Basin, Chiu uses a ViroChip to see how viruses mutate over time. The three-inch glass slide has thousands of spots of DNA from almost all known viruses. Swine flu, he said, hasn’t seen any changes yet – but he’s keeping a careful eye on it.

“The virus could potentially become as virulent as the 1918 flu virus,” said Chiu.

“The good news is that we haven’t seen any mutation so far,” Dr. Chiu said, adding that the swine flu seems to mutate more slowly than the seasonal flu, which required new shots every year because of it’s antigenetic shift, or small changes that make a virus resistant to a vaccine.

There’s always something to worry about.

The other possibility for mutation is called antigenetic drift. That’s when viruses meet, mix, and become stronger. The seasonal flu has been virtually replaced by swine flu but Dr. Chiu and other researchers are watching out for cases where swine flu and seasonal strike a person at the same time. That combination could cause a mutation, but Dr. Chiu said there have been no more than five such flu victims and no mutations observed.

The other kind of mutation could bring birds into the picture. “The swine flu virus could mix with bird flu and produce an entirely new strain that may be extremely virulent or deadly,” said Dr. Chiu.

Chiu says the reason for the recent uptake in southern states like Georgia, South Carolina, and Alabama could likely be due to low vaccination rates there. A study released April 2 by the US Centers for Disease Control and Prevention found that about 24 percent of the country has been vaccinated. Georgia has among the lowest vaccination rates in the country. California is in the middle, with a third of children and 18 percent of adults immunized.

A Walgreens spokesperson said vaccinations have slowed down since mid-January. A Safeway pharmacist said vaccinations there have dropped by half in the past five weeks. Maxim Health Systems, a mobile immunization clinic that administered over 3,100 swine flu shots at 59 clinics in San Francisco in the past three months, has slowed to a stop.

"H1N1 Flu Shot Here Today." The Walgreens on 16th and Mission.

The uptake in the Southeast could also be the beginnings of a third wave making its way west. Last year, the Southern states were hit by a second wave in August, while California experienced its second wave in October.

“The more people are vaccinated, the less likely we’ll see another wave,” said Dr. Chiu. The vaccine comes in the form of a nasal spray or an injection. The US Centers for Disease Control and Prevention is working on a vaccine for the end of this year, which will combine the seasonal vaccine with the swine flu vaccine.

“It’s our hope that this vaccine will remain effective for some time – whether it’s effective next year depends on mutation,” he added.