Trump political appointees tried to silence a longtime top official at the Centers for Disease Control and Prevention after she stressed the seriousness of the coronavirus, arguing her statements to a medical group contradicted those of top Trump administration officials, including Vice President Pence.

In a June 30 email, Paul Alexander, one of those appointees at the Department of Health and Human Services, excoriated Anne Schuchat, CDC principal deputy director, for remarks she made before the group affiliated with one of the nation’s leading medical journals. Schuchat, a physician, had spoken to JAMA Network the day before, saying she hoped the country could “take it seriously and slow the transmission,” adding that “we have way too much virus across the country … right now.” The emails were first reported by the New York Times.

Schuchat’s comments came as cases were surging across several southern and western states — even as the president and his top advisers were intent on reopening the country and boosting the economy. But Alexander wrote to his boss, Michael Caputo, assistant secretary for public affairs at HHS, reprimanding Schuchat and writing a seven-point takedown of her assessment.

“Her comments are in contrast to those of senior members of the Trump administration — notably Vice President Pence, who said on Friday, ‘we have made truly remarkable progress,’" Alexander wrote.

“Importantly, having the virus spread among the young and healthy is one of the methods to drive herd immunity,” Alexander added. “She is duplicitous.”

Both Caputo and Alexander are now gone. But their emails offer new insight into how they created their own power center at the agency overseeing the pandemic response and used it to censor, and even humiliate, top scientists and health officials in an effort to sideline them or make them conform to White House-sanctioned messages. The tone of the emails is often emotional and accusatory, and they put more emphasis on the political import of the messages than on their medical or scientific substance, even as the virus raged out of control.

Caputo, a Trump loyalist engulfed in controversy, left on a 60-day medical leave earlier this week after a bizarre Facebook rant in which he accused government scientists of “sedition” and warned supporters to take up arms to prepare for violence after the election. Alexander, a Canadian PhD he had hired on contract, was permanently let go this week, HHS said in a statement.

When asked for comment on the emails via text, Caputo responded with a thumbs down emoji. Alexander did not respond to a request for comment.

An HHS spokeswoman said Caputo was trying to ensure proper protocols were followed for interviews with public health officials — protocols that the spokeswoman said predate the Trump administration. HHS is the parent agency of CDC, the Food and Drug Administration, the National Institutes of Health and the Centers for Medicare and Medicaid Services.

Caputo, a longtime Buffalo political consultant who had worked on behalf of people in Russia and Ukraine, as well as in the U.S., had previously remarked on how critical the virus was to Democratic hopes of defeating President Trump in November.

On a March 13 episode of his podcast, “Still Standing,” shortly before he was hired to work at HHS, Caputo suggested that Democratic candidate Joe Biden’s only assets against Trump would be the coronavirus pandemic and the tanking economy that resulted.

“It’s very clear they’re counting on two things: fatalities, of course. Fatalities,” Caputo said in the podcast. “Because the more people that die, the more personal tragedy there is. And that’s emotional and it gives Democrats a chance to harvest, let’s just say, waning enthusiasm in the president. A lot of people die, the Democrats win.”

Alexander’s attempts to order career civil servants to rewrite CDC guidance, or instruct them on what they should or shouldn’t say quickly caused friction after he joined HHS this spring as Caputo’s adviser. He also instructed Anthony S. Fauci — the top government infectious-disease expert who has led the U.S. response to numerous epidemics — that he should refrain from advocating that children wear masks. Fauci disregarded his advice.

Caputo and Alexander also sought more control over the CDC’s weekly scientific missives, called the Morbidity and Mortality Weekly Report. Caputo told The Washington Post he was frustrated they could only see summaries ahead of publication, rather than full drafts.

In an unusual step, Schuchat authored a report in May that described how the virus first arrived in January, then began spreading rapidly in multiple parts of the country by mid-March. Schuchat does not often author reports by herself, and the report took senior HHS leaders by surprise.

Azar called CDC Director Robert Redfield shortly after the report’s publication in a heated exchange to express frustration over procedural issues at CDC, including the way Schuchat’s report took senior leaders by surprise, according to a senior HHS official. In the call, Redfield echoed Azar’s frustrations that they did not have more notice ahead of publication, the official said.

But Caputo and Alexander went much further than Azar and other senior HHS leaders by seeking full control over the reports, several agency officials said.

Alexander also criticized Schuchat for saying in the JAMA interview that for most people, covid-19, the disease caused by the novel coronavirus, causes mild or moderate symptoms that clear up in two to three weeks. But she noted that in older adults and people with preexisting health conditions, including children, it could cause more severe illness and death.

“It also causes no symptoms as it is so mild … you don’t even know you have it,” Alexander wrote in his critique. “Many people never know they had it. Not one indication. It is very false her statement that it causes death in children … Based on CDC’s own data, the risk of death in children 0-19 years of age is basically 0 (zero) … PERIOD … she has lied here.”

In fact, several studies have shown that children can develop severe complications from the virus which can cause life-threatening and lasting complications, and a small number have died.

Schuchat, who could not be reached for comment, has more than three decades of experience at the CDC, and is well regarded inside the agency, within HHS and by lawmakers. She has played key roles in many public health emergencies, including the 2009 swine flu epidemic, the 2003 outbreak of severe acute respiratory syndrome (SARS) and the 2001 anthrax attacks in the United States.

Tom Inglesby, director of the Center for Health Security at the Johns Hopkins Bloomberg School of Public Health, said Alexander has no real-world experience responding to a health crisis on this scale. “It is complete nonsense for someone who has not worked on preparing for, or responding to epidemics or pandemics before … to say he knows better than Fauci and CDC when it comes to the response to this pandemic,” he said.

Alexander, who was previously a caller to Caputo’s onetime Buffalo radio show, holds a doctoral degree in health research methodology from McMaster University in Hamilton, Canada, according to his résumé. His doctoral dissertation looked at ways to use data to make effective recommendations for clinicians and public health officials when confidence in the data is low.

An unpaid assistant professor at McMaster, he has previously worked for the Infectious Diseases Society of America and consulted for the World Health Organization. On his résumé, he calls himself an “expert in evidence-based, evidence informed medicine.” McMaster distanced itself from Alexander this week.

Inglesby said responding in real time to a pandemic is much different than the academic application of health guidelines.

“In this pandemic, there are many new things happening for the first time,” he said, “many decisions that need to be made in the setting of uncertainty, perhaps on the basis of unfolding information, research that is in progress or at a time when we don’t yet have the complete story.”

The Washington Post first reported on Alexander’s attacks on the CDC in July.

“The CDC is undermining the President by what they put out, this is my opinion and sense, and I am reading it and can see the subtle and direct hits,” he wrote in one email.