Dr. Jake Scott is on the front line of his second pandemic in five years and he is not getting much sleep.
Scott works full-time as an infectious disease physician at Stanford Health Care’s Tri-Valley hospital in Pleasanton, California. When he is done taking care of his patients and his two grade-school aged kids, he often stays up past midnight writing — furiously penning op-eds, collecting studies, leading evidence reviews and posting meaty threads on social media, most of them correcting the record on vaccines.
Often, he’s reacting to the latest maneuvers by US Health and Human Services Secretary Robert F. Kennedy Jr.. A pinned post responding to one of Kennedy’s appearances on Fox News has been viewed almost 5 million times. Another post fact-checking Kennedy’s claims about potential harms from aluminum in vaccines had 1 million views in its first 48 hours. Scott’s followers on X have doubled since April.
“A million views for this long-winded, very detailed, kind of nerdy breakdown of the science,” Scott said, marveling at the attention it got. “I think that’s saying something, you know? People want that information, and they deserve it,” said Scott who is 48.
The Covid-19 pandemic turned many infectious disease specialists and virologists into household names. Scott’s was not one of them, perhaps because he was too busy treating patients. He didn’t stay out of the public discourse completely, however. He was one of the first doctors to tell people that Omicron didn’t seem to be as severe an infection as earlier strains of the virus, although some virologists were skeptical at the time.
In President Donald Trump’s second administration, however, Scott is taking on what he sees as a second pandemic — misinformation and disinformation about vaccines. He knows false information can be as harmful as any virus.
“When officials spread inaccurate information about vaccines, it does have real consequences, and families make decisions based on fear rather than on facts,” Scott said.
It’s already happening. The US Centers for Disease Control and Prevention recently reported data showing kindergarten vaccination rates continue to decline, as states make it easier to opt out of school vaccination requirements. Vaccine preventable diseases like measles and whooping cough are rising again, too.
Scott knows it could get much worse.
“In 2021, nearly every single patient I lost to Covid was unvaccinated by choice, and every colleague of mine has said the same thing.”
A pandemic within a pandemic
For Scott, the fight to restore trust in vaccines is deeply personal.
In 2020, he found himself in the crosshairs of Covid-19, treating a deluge of patients —many of them young and healthy — for a lethal new virus that was eating up their lungs, clotting their blood and causing catastrophic immune reactions.
In the beginning, they had nothing to stop it. No tests, no treatments, and certainly nothing to prevent it. He worked all day, every day during the week and every other weekend in full personal protective equipment. He says he lost dozens of patients in the span of a few months. He kept track of the numbers for a while, but then stopped counting when the deaths became so frequent.
“We tried so hard,” Scott said in an interview with CNN. “Despite fighting for my patients with a hundred percent dedication, I lost so many people.”
Then, in late December, 2020, it felt like a miracle happened — the Covid-19 vaccine. Operation Warp Speed had delivered what Trump had promised: a safe and highly effective vaccine in less than a year.
“I can’t emphasize enough how dramatic that change was once the vaccines became available,” Scott said. “I did see it firsthand, and it was mind-blowing.”
Within weeks, a Covid diagnosis was no longer a death sentence — at least, for the vaccinated. Even his most fragile patients, elderly people living in nursing homes, stopped dying. And then, as the vaccine became widely available, Scott’s crushing patient load lightened.
But even as science was finally making inroads against Covid, a second problem arose, a phenomenon the World Health Organization identified as an infodemic—the flood of information, much of it false, that occurs during a disease outbreak.
“We had these two parallel pandemics. We had the Covid pandemic, and then the pandemic of, you know, the infodemic misinformation,” Scott said.
While Covid is no longer a public health emergency, Scott said, the country never effectively dealt with the disinformation pandemic, and we’re paying for it now.
He believes misinformation, more than almost anything else, explains our current political moment, and “it’s only getting worse,” he said.
“I’ve seen what happens when people avoid vaccines because of misinformation, and it’s absolutely heartbreaking,” Scott said.
Scott has made it his mission to take on misstatements and distortions about vaccines, especially when they come from Kennedy, a longtime anti-vaccine activist who Trump installed as his Secretary of Health and Human Services earlier this year.
He is doing it at a time when many others are afraid to speak up for fear of making themselves or their institutions targets of the Trump administration’s lawsuits and funding cuts, and when anti-vaccine rhetoric and demonization of scientists has inspired violence.
“I’m not afraid,” Scott said. “Stanford stands behind me. I have amazing support.”
Kennedy has maintained that he is not anti-vaccine and that he is a proponent of vaccine safety. But Kennedy’s HHS has already made sweeping changes to US vaccine infrastructure and policy.
Scott says he has not heard directly from Kennedy, but he does get comments from his supporters. Some have called Scott “brainwashed” and a “pharma shill” or accused him of being “a fake doctor.” (The University of Vermont confirmed Scott graduated from medical school there in 2011, and he has an active medical license in California.)
Scott said he gets a salary from Stanford to treat patients and teach, but he’s mostly working to correct the record on vaccines on his own dime. The government’s Open Payments database — where drug companies have to report payments to physicians — shows Scott received a single payment between 2018 and 2024, a $13 payment reported by the drug company Janssen in 2022. Scott thinks he must have eaten a group lunch somewhere and didn’t realize it was sponsored.
Scott’s writing and advocacy recently caught the attention of Dr. Michael Osterholm, who directs the Center for Infectious Disease Research and Policy at the University of Minnesota. Osterholm tapped him to be a senior reviewer of evidence for the Covid, flu and RSV vaccines for the Vaccine Integrity Project, a group of outside public health experts that has been independently reviewing data on vaccines out of concern for vaccine misinformation and access under current federal health leadership.
Scott cancelled a planned vacation to jump in to help and was among the scientists who presented the group’s findings live on YouTube on Tuesday.
“He has an uncanny way of taking complicated issues and distilling them down into readable, understandable pieces of information,” Osterholm said. “He has what I consider to be almost limitless energy. He’s really a very hard worker.”
“He is a real professional star,” Osterholm said, “But personally, he’s just, he’s a very kind and thoughtful individual.”
“I work with a number of colleagues, even now, who never had a job until they became doctors,” Scott said, “And you can kind of tell. They’re still great doctors, but it’s just a different perspective.”
Scott got his first paying job at age 11, an off-the-books gig at A Bicycle Odyssey, a bike shop in Sausalito, California, frequented by the likes of Robin Williams, members of the band The Grateful Dead and Huey Lewis. He said the owner paid him $2.50 an hour to organize bike shoes. Eventually, he graduated to lacing the spokes on bike wheels.
Scott said he didn’t save much because he poured all his earnings back into the shop.
Becoming a doctor was never something he imagined he could do.
His parents were hippies, Scott said. They bought a fishing shack in Sausalito, one of the few properties that had its own beach, and over years of living there turned it into a two-story house.
Scott’s parents were well-known and liked in Sausalito. They started a July 4 parade in town. His father was on the local school board and often walked around town with a parrot on his shoulder. He owned a business that distributed the print edition of The New York Times around the San Francisco Bay area.
“Both our kids have worked all their lives. They had no choice,” said Scott’s father, Marvin.
After Scott’s stint at the bike shop, he went to work at a surf shack at age 14, a hobby that became another passion. For college, he followed his older sister to the University of California at Santa Cruz because there was good surfing near the campus.
For the first two years, he said he dabbled in different interests, including environmental studies. Realizing he didn’t know what he wanted to do with his life, and not wanting to waste money on tuition, he took a year off from school and worked roofing and construction jobs. For a while, he said, he lived in the woods behind the campus.
The hard, physical labor of construction convinced him to return to school.
“I wanted to use my brain, not my back,” he said.
He began writing poems and short stories and applied to the literature program. He got in and graduated with a writing degree.
After gradulation he worked odd jobs and traveled. He taught English in Japan, but nothing seemed to stick or turn into a career.
When he came back to the US, a friend recruited him to work at Planned Parenthood. He worked as a medical assistant — talking to patients, often guiding them through the most difficult times in their lives — and became an HIV testing counselor. He discovered he had a talent for it.
“A lot of clients were surprised when they when they found that their medical assistant was a man,” Scott said. “But I think that that really taught me to try to sort of be disarming and not judgmental and not intimidating, and to be empathetic.”
He volunteered at San Francisco General Hospital and worked in the Tenderloin, a part of the city that’s had a reputation for drug use, crime, and homelessness, helping with needle exchange programs for people with substance use disorders.
“He fell in love with medicine,” Marvin Scott said of his son.
The experience at Planned Parenthood made him think about becoming a doctor, even though it was never a dream he’d had for himself.
“It was a pretty gutsy thing to do at that stage in his life,” said Scott’s dad, Marvin. His parents gave their blessing — as long as he paid for it himself.
There was just one problem: Scott hadn’t taken any pre-med classes in college. The only biology class he took in college was an intro to marine biology called “Life Under the Sea.”
He enrolled in a two-year program at Mills College, traditionally a women’s college, for graduates who wanted to go to medical school.
“I worked so hard,” Scott said. The school’s library closed at midnight, and Scott says he was usually there when they were locking up.
“I had sort-of avoided science and math growing up. I was just this free-spirited kid and young adult,” Scott said. “I didn’t know whether I had what it takes to be a doctor.”
As he was completing his studies at Mills, he ran the gauntlet of med school admissions, applying to dozens of schools and flying around the country for interviews. He was accepted to the University of Vermont and started medical school at age 30.
“I think my sort of secret weapon is that I have a lot of self-discipline. And I don’t think of myself as the smartest by any means, but I do have a pretty, pretty insane work ethic,” Scott said.
After two years of learning anatomy and taking classes exams in medical school, Scott spent two years shadowing country doctors in Maine and Vermont, sometimes making house calls to see patients.
One of them, a doctor known to be a tough evaluator, later wrote Scott a recommendation saying that not only was he well-informed and great with patients, but “He’s got soul.”
“That just meant so much to me,” Scott said.
As a medical resident — essentially a junior doctor — at the Kaiser Foundation Hospital in Oakland, Scott got to try out different specialties. One of his first rotations was infectious disease.
His first patient — a wealthy, older White man — was gravely ill in the intensive care unit. His case had stumped his doctors. He was anemic, with high fevers and a high heart rate. He had all the symptoms of malaria, but none of the risk factors.
The infectious disease team was called in to consult on the case. The doctor who was training Scott thought of a disease that mimics malaria, called Babesiosis. It’s caused by a parasite that infects red blood cells through the bite of a tick.
But the ticks in California, where the man lived, don’t commonly carry Babesia. The infection was more widespread in New England.
The doctor asked the man’s wife if they had been there recently.
“Sure enough, a week before he came in, they had spent the summer on Long Island,” Scott said. They checked the patient’s blood under a microscope. The cells were teeming with parasites.
“She made the diagnosis by asking this one question,” he said.
Infectious disease seemed like the perfect combination of Scott’s academic interests —medicine and storytelling. If you could understand a patient’s story, oftentimes, you could make a diagnosis. Scott was hooked.
He got his dream job at Stanford, one of the best infectious disease programs in the world.
Then it was 2020, and his dream job became a nightmare.
“I just can’t emphasize enough how devastating 2020 was,” Scott said. He watched people die of a virus, then watched others die because they couldn’t separate facts from fiction and were too scared to get a vaccine.
He remembers treating a family of three, all unvaccinated, and all three got severe Covid. None had any significant underlying medical conditions.
The father told Scott that he’d rather be shot in the head than get the Covid-19 vaccine. The mother didn’t survive her infection. When the son woke up in the ICU, he learned she had died.
“It was one of the worst things I’ve ever experienced,” Scott said.
“I saw her as a victim of inaccurate information,” Scott said. “I remember seeing family members crying outside of the hospital, and they were holding bags with her belongings, and it absolutely broke my heart.”
So he’s staying up at nights working late, hoping to save others from the same fate:
No, children don’t get 92 shots by the time they’re 18, he explained recently on X. Even if you count annual flu shots, it’s about 48 to 51.
Yes, we do know the safety profiles of vaccines, he shared in another post.
No, the people who made recommendations about vaccines to the CDC — before they were dismissed by Kennedy — don’t have rampant conflicts of interest, he detailed in another post.
In that way, he hopes to inoculate people against disinformation, one fact at a time.
