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On June 30, as the coronavirus was cresting toward its summer peak, Dr. Paul Alexander, a new science adviser at the Department of Health and Human Services, composed a scathing two-page critique of an interview given by a revered scientist at the Centers for Disease Control and Prevention.

Dr. Anne Schuchat, a 32-year veteran of the CDC and its principal deputy director, had appealed to Americans to wear masks and warned, “We have way too much virus across the country.” But Alexander, a part-time assistant professor of health research methods, appeared sure he understood the coronavirus better.

“Her aim is to embarrass the president,” he wrote, commenting on Schuchat’s appeal for face masks in an interview with the Journal of the American Medical Association.

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“She is duplicitous,” he also wrote in an e-mail to his boss, Michael Caputo, the Health and Human Services Department’s top spokesman who went on medical leave this week. He asked Caputo to “remind” Schuchat that during the H1N1 swine flu outbreak in 2009, thousands of Americans had died “under her work.”

Of Schuchat’s assessment of COVID-19’s dangers, he fumed, wrongly, “The risk of death in children 0-19 years of age is basically 0 (zero) … PERIOD … she has lied.”

Alexander’s point-by-point assessment, broken into seven parts and forwarded by Caputo to Dr. Robert Redfield, the CDC director, was one of several emails obtained by The New York Times that illustrate how Caputo and Alexander attempted to browbeat career officials at the CDC at the height of the pandemic, challenging the science behind their public statements and attempting to silence agency staff.

Far from hiding what they knew about the virus’s danger, as Bob Woodward’s new book contends President Donald Trump was doing, the emails seem to indicate that aides in Washington were convinced of their own rosy prognostications, even as coronavirus infections were shooting skyward.

At the same time, Caputo moved to punish the CDC’s communications team for granting interviews to NPR and attempting to help a CNN reporter reach him about a public-relations campaign. Current and former CDC officials called it a five-month campaign of bullying and intimidation.

For instance, after Caputo forwarded the critique of Schuchat to Redfield, CDC officials became concerned when a member of the health department’s White House liaison office – Catherine Granito – called the agency to ask questions about Schuchat’s biography, leaving the impression that some in Washington could have been searching for ways to fire her.

In another instance, Caputo wrote to CDC communications officials July 15 to demand they turn over the name of the press officer who approved a series of interviews between NPR and a long-time CDC epidemiologist, after the department in Washington had moved to take ownership of the agency’s pandemic data collection.

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“I need to know who did it,” Caputo wrote. A day later, still without a reply, Caputo wrote back. “I have not received a response to my e-mail for 20 hours. This is unacceptable,” he said. “I need this information to properly manage department communications. If you disobey my directions, you will be held accountable.”

On Wednesday, Caputo went on leave from the department, just days after he attacked CDC scientists during a bizarre Facebook video in which he predicted armed insurrection after the election and encouraged his followers to stock up on ammunition.

CDC scientists “haven’t gotten out of their sweatpants except for meetings at coffee shops” to plot “how they’re going to attack Donald Trump next,” Caputo said in the video.

The department also announced that Alexander would leave the government.

On Friday, a department spokeswoman referred the Times to its Wednesday statement announcing Caputo’s leave and Alexander’s departure. She added that Caputo, in his comments about interview approvals, had been trying to make sure that the CDC followed protocols dating to prior administrations that the department clear interview requests for health officials. The CDC did not have an immediate comment nor did Caputo.

In the months leading up to their exits, the two had routinely worked to revise and delay the CDC’s closely guarded and internationally admired health bulletins, called Morbidity and Mortality Weekly Reports, in an effort to paint the administration’s pandemic response in a more positive light.

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Far from apologetic, Alexander told The Globe and Mail this week that the CDC had written “pseudo-scientific reports” and that he was better suited to examine data than agency scientists.

“None of those people have my skills,” Alexander said. “I make the judgment whether this is crap.”

The judgments he rendered – and the punishments that Caputo appeared intent to mete out – had a demoralizing effect on the agency.

One CDC communications official became so worried about Caputo’s threat that she wrote to other senior staff asking how to reply, saying that she was “uncomfortable turning over our employee’s name to Mr. Caputo, given the hostility of the message.”

In another e-mail to an agency communications officer who had directed a CNN reporter to contact Caputo about a vaccine public relations campaign, Caputo shot back, “In what world did you think it was your job to announce an administration public service announcement campaign to CNN?”

The CDC press official then apologized, which did not satisfy Caputo. “We will discuss this on a teleconference tomorrow. I want your H.R. representative in attendance,” he wrote. He then scolded the official for removing Redfield from the email thread after Caputo had added the director in a prior e-mail.

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In the emails obtained by the Times, Caputo repeatedly added Redfield, who was overseeing an 11,000-person agency, to e-mail chains about news media disputes. People familiar with the emails said it was an attempt to use Redfield to shame his own staff.

People familiar with Redfield’s responses to the emails said that he would call senior aides sounding resigned to the orders and asking how to navigate Caputo’s demands. Often, he tried to delay or ignore Caputo until the tension subsided.

Perhaps most illuminating in the emails was the way the top officials at the CDC saw the illness in fundamentally different ways than confidants and loyalists of Trump. In the interview that provoked Caputo and Alexander, Schuchat referred to “a lot of wishful thinking around the country that, ‘Hey, summer, everything is going to be fine, we’re over this.’

“And we are not even beginning to be over this,” she said. “I think we need to continue to learn and continue to apply what we’re learning and be humble about our assumptions.”

At the time of her interview, the nation was setting record levels of new infections and was weeks away from an even more catastrophic peak of almost 70,000 new cases a day. States such as Arizona were pausing the reopening of their businesses.

Dr. Anthony Fauci, the government’s leading infectious disease expert, testified to a Senate panel that the country could hit 100,000 new cases a day.

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That portrait of the virus was at odds with the one the White House had strained to present. The day Schuchat lamented there was “way too much virus across the country,” Kayleigh McEnany, the White House press secretary, told reporters, “we’re aware that there are embers that need to be put out.”

Trump said in an interview with Fox Business Network that week that he believed the virus was “at some point” going to “sort of just disappear, I hope.”

Alexander also had his own ideas of the virus’s staying power. He disputed Schuchat’s claim that children were vulnerable to it. Studies have repeatedly demonstrated that while it is rare, the virus can be lethal to children, who can readily transmit it to more vulnerable family members.

“It also causes no symptoms as it is so mild … you don’t even know you have it,” Alexander wrote. “Many people never knew they had it. Not one indication. It is very false her statement that it causes death in children.”

At one point in his response to Schuchat, Alexander appeared to endorse the largely rejected strategy of “herd immunity,” or allowing the virus to freely spread until enough people develop antibodies that it dies for lack of human hosts.

“Importantly, having the virus spread among the young and healthy is one of the methods to drive herd immunity,” he wrote. “This was not the intended strategy but all must be on deck now and it is contributing positively at some level.”

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The clashes between the White House and CDC intensified this week, when Trump publicly slapped down congressional testimony Redfield gave, in which he praised masks and estimated that a vaccine might not be widely available to the public until the middle of 2021.

“I think he made a mistake when he said that,” Trump told reporters. “It’s just incorrect information.” A vaccine would go “to the general public immediately,” the president insisted, and “under no circumstance will it be as late as the doctor said.”

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