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That portrait of the virus was at odds with the one the White House had strained to present. The day Dr. 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.”

Mr. 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.”

Dr. Alexander also had his own ideas of the virus’s staying power. He disputed Dr. 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,” Dr. 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 Dr. Schuchat, Dr. 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.”

The clashes between the White House and C.D.C. intensified this week, when Mr. Trump publicly slapped down congressional testimony Dr. 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.