At Brigham and Women's Hospital, a code amber alert sounded.
"It is basically a disaster notification that we use when we have a large number of things to deal with," Dr. Walls said. "It freezes the staff so basically no one is going to be allowed to go home."
In one afternoon, Walls' section of the ER saw eight patients, more than four times what they typically see this time of year.
"The big difference I think that I've seen this year is that there is so many more people with it," Walls said. "So we talk about the virulence of the flu, like how fast can it get from me to you and from you to someone else. This flu seems to have spread from really rapidly through large, large numbers of people."
One of his biggest concerns was elderly patients, who are also at high risk of complications from the flu. Eighteen people over age 65 have already died from the flu in Massachusetts.
Many doctors still agree that the best weapon of defense against the flu is to get a flu shot. An East Boston neighborhood health center said they have given 20,000 flu shots this season and more than 700 alone on Saturday.
"We don't usually have to do big clinics like this but when there's a need, particularly like this when the flu is so severe, we really want to vaccinate people, we're happy to do this," said Dr. Catherine Silva, a local primary care physician.
Concerned parent Tequila Cunningham, who was waiting for her flu shot at the health center, said she wasn't taking any chances.
"There has been four episodes of kids getting sick in their school," she said. "I feel like the flu shot and some vitamin C and they're going to be great."
On Sunday, Cassie was still at Children's Hospital and had been moved into intensive care. She had to have mucus drained from her lungs but was slowly starting to improve.
"I think we might be able to get her home soon," Meghan Moriarty said.
But the ordeal has taken its toll and Cassie's mother was exhausted.
"I actually fainted last night," she said. "I forgot to feed myself."
But after 24 hours, Mass General patient Shane Wells, who felt awful after being discharged, said he was starting to feel a lot better
"I pretty much feel 80 percent," he said. "I'll make it back to work tomorrow, I'm feeling good now. I'll get a good night's sleep, keep taking my medicine and I think I'll be all right."
Boston-area hospitals reported a decline in flu admissions over the weekend, suggesting things are looking up in a city that is sick of being sick.