WASHINGTON – 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 an experienced CDC scientist.

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

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

“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 in the 2009 swine flu outbreak, thousands of Americans 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.”

His assessment, forwarded by Caputo to Dr. Robert Redfield, the CDC director, was one of several e-mails obtained by the New York Times that illustrate how Caputo and Alexander attempted to browbeat CDC career officials, challenging the science behind their public statements and attempting to silence CDC staff.

On Friday, two days after Caputo went on medical leave and Alexander was dismissed from the Health and Human Services Department, the CDC reversed a heavily criticized recommendation suggesting that people who have had close contact with a person infected with the coronavirus do not need to get tested if they have no symptoms. The e-mails shed light on the monthslong fight that led to their departures.

Far from hiding what they knew about the virus’s danger, as Bob Woodward’s new book contends President Donald Trump was doing, the e-mails 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 longtime CDC epidemiologist after the department in Washington had moved to take ownership of the agency’s pandemic data collection.

“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 email 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 Friday, a department spokeswoman said 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.

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

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.”