Some Bay Area hospitals and pharmacies began reporting temporary vaccine shortages Friday, just as California health officials sounded the alarm over the recent spate of swine flu deaths and urged people to get vaccinated.

State officials said they weren’t aware of any such shortages, but corporate spokesmen for both CVS and Walgreens on Friday confirmed that some stores had run out of flu vaccines because of the high demand — and that it would take about 48 hours to get new supplies.

At Kaiser Permanente’s Santa Clara hospital, the lines for flu shots for adults and children were both 20 deep Friday afternoon, while other Bay Area residents rushed into their local pharmacies.

Two more H1N1 “swine flu” deaths were reported Friday by Alameda County, bringing the county’s recent toll to three. Seven Bay Area counties and Santa Cruz County have reported 13 deaths, including a 23-year-old Sonoma County man who had no apparent underlying health problems.

“When young people start dying, you kind of start taking it seriously,” said 65-year-old Roanne Hobizal, among those lined up for a flu shot at a Pleasanton Safeway pharmacy on Friday afternoon.

H1N1 appears to be the predominant strain so far this flu season, and that concerns state health officials because unlike other influenza strains, swine flu can result in lethal pneumonia even in young, healthy people.

During the 2009-10 flu season, at least 203,000 people died worldwide in the swine flu pandemic, including more than 600 Californians.

At Kaiser Santa Clara, Dawna Dougherty waited for her shot with her three sons: Jacob, 12, Scott, 10, and 8-month-old Jack. The Santa Clara resident said the family went to Kaiser after hearing news reports about flu deaths and worrisome accounts from a friend who works in a hospital emergency room.

“She has seen lots of flu infections in otherwise healthy adults,” Dougherty said. “I don’t want to end up in the emergency department barely able to breathe.”

The long wait for flu shots around the Bay Area was good news to state public health officials, who during a Friday morning news conference warned that the number of fatalities in California is rising rapidly and “exceeding what is expected for this time of year.”

“If we get more people to get vaccinated now, I can assure that the curve (in numbers) will abate, and we will prevent many more illnesses,” said Dr. Gil Chavez, a deputy director of the California Department of Public Health.

A Kaiser spokesman said the hospital system has experienced some spot shortages of vaccines but is moving supplies between facilities to meet demand. Kaiser has also ordered thousands of additional doses from suppliers and expects to receive them starting Monday.

Dan Jardin, a pharmacist at Raley’s in Pleasanton, said Friday was the busiest day for shots since flu season began in September.

“I’m spending so much time here, I may as we’ll just sleep here,” he quipped, as five customers sat waiting for a shot. Jardin said the store was not facing any shortages of the vaccine.

But at a nearby CVS, a pharmacy tech said the store had run out and wouldn’t be getting any more flu vaccine until Thursday.

While county health officials around the state have been reporting flu-related deaths since the new year began, the state on Friday confirmed only those flu deaths through Jan. 4, the halfway point of the flu season that begins in late September.

Only seven deaths were recorded through that date, even though counties have reported at least 28 since then.

The flu fatalities confirmed by the state were in Alameda, Contra Costa, San Francisco, Sacramento, Los Angeles, Lassen and Stanislaus counties. All but one was attributed to the H1N1 virus, Chavez said.

After the swine flu pandemic of 2009-10, California required influenza deaths in people under 65 to be reported to the state’s public health department, so the number of flu-related deaths at the end of the flu season could actually be higher.

“The purpose of reporting flu deaths under 65 is because with flu, that’s a good indicator of the severity of the flu season,” said Dr. Sara Cody, Santa Clara County’s public health director. “You don’t expect people under 65 to land in the ICU or die from the flu.”

While an uptick in flu cases is expected in January and February, Chavez noted that it’s “trending up a little earlier than last year.”

State figures show that the swine flu pandemic that hit in 2009-10 resulted in the deaths of 607 people, 539 of them under age 65.

In 2010-11, reported flu deaths totaled 89; in 2011-12, it was 51; and in 2012-13, 106 people under 65 died of the flu.

Traditional flu strains hit older people more severely, Chavez said, “but H1N1 does not discriminate on the basis of age. Everyone may have a bad outcome.”

State health officials say shots are recommended for those 6 months or older, and particularly for those people at higher risk of severe influenza, including the elderly, pregnant women and anyone with underlying medical conditions. The vaccine takes about two weeks before it becomes effective.

Standing next to the elevators at Kaiser Santa Clara, Dougherty and Jacob made windmills with their arms that had just been injected.

“I don’t like shots,” Jacob said. “Yeah, it hurt.”

His brother disagreed.

“Didn’t feel a thing,” Scott said.

“I’m not an alarmist,” said their mother. “I’m not worried about death from the flu. I’m worried about serious illness. I don’t want the whole family getting sick.”

Contact Tracy Seipel at 408-920-5343. Follow her at Twitter.com/taseipel.