NEW YORK (CBSNewYork) — New fears are mounting about the flu, with people rushing to get protected and finding that providers are running out of the vaccine.

As CBS2’s Jessica Layton reported, the rush to heed warnings to get vaccinated near the peak of one of the worst flu seasons on record has resulted in an unexpected problem.

“Well there’s shortages actually throughout the city, and you call around to pharmacies and you’ll find difficulty getting the flu vaccine — especially for children,” said Dr. Robert Glatter of Northwell Health Lenox Hill Hospital.

CBS2 checked with 12 pharmacies in Manhattan and Westchester County. They all said they were out of vaccine and did not know when or if they would get more.

Some smaller independent pharmacies did have some vaccine in stock, but were having trouble keeping up with the demand.

“It’s very difficult to speed up production,” Glatter said. “It takes a certain amount of time — 90 days — to make one batch. So there’s a lag right now.”

The surge to get the shot comes upon learning that the flu has led to the deaths of nearly 40 children across the country this season – including an unvaccinated 4-year-old from central New Jersey in December.

Doctors’ offices and pharmacies have also reported they are running out of the antiviral Tamiflu, which can shorten the virus by a couple of days when taken within the first 48 hours of symptoms.

“They are less likely to suffer complications of influenza such as encephalitis, pneumonia,” said Dr. Amy Edwards, who specializes in pediatric infectious diseases at University Hospitals Rainbow Babies & Children’s Hospital.

The push to protect is in full swing in Minneapolis, as millions of fans flock to that city for Super Bowl activities. Organizers of those events are busy disinfecting and wiping down equipment, with doctors warning those who do go to the game that they may be entering a petri dish of germs.

“Think of influenza like a lottery,” said epidemiologist Mike Osterholm. “If a normal day you’d only come in contact with 10 people, that’s one chance — 100 or 1,000, you just upped your chances that much more.”

If your doctor’s office of pharmacy are out of the vaccine, keep calling. A few of the pharmacies Layton visited Wednesday night said they hope to get more in next week.

In the meantime, doctors stress it is important to go the extra mile and take care of yourself.