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U.S. officials are preparing to battle two bad viruses circulating at the same time as the coronavirus outbreak runs into flu season next fall and winter.

The Covid-19 outbreak in the U.S. hit just as the flu season was ending this year, Robert Redfield, director of the Centers for Disease Control and Prevention, said at a White House press briefing Wednesday. But they won't have that benefit of using the country's flu surveillance system to track the Covid-19 pandemic when the next flu season hits, he said.

"Next fall and winter, we're going to have two viruses circulating and we're going to have to distinguish between which is flu and which is the coronavirus," Redfield said.

But Redfield noted that he didn't say the coronavirus itself would be "worse" in the winter.

Earlier in the press conference, President Donald Trump said Redfield was "totally misquoted" when he previously said challenges from the coronavirus could be "more difficult" in the winter.

"He was talking about the flu and corona coming together at the same time," Trump said, "and corona could be just some little flare-ups that we'll take care of."

Redfield told The Washington Post on Tuesday that the already daunting task of responding to the coronavirus outbreak could only become more challenging in the winter, when flu season begins.

"There's a possibility that the assault of the virus on our nation next winter will actually be even more difficult than the one we just went through," Redfield told the Post. "And when I've said this to others, they kind of put their head back, they don't understand what I mean."

"We're going to have the flu epidemic and thecoronavirusepidemic at the same time," the newspaper reported him saying.

The headline of the newspaper's story read: "CDC director warns second wave of coronavirus is likely to be even more devastating." Trump called that headline "ridiculous" and "fake news" at the briefing Wednesday evening.

"It's possible if the corona even comes back" in the winter, Trump said, "and [Redfield] doesn't know that it's going to and neither do I ... we may have some embers [of the virus] and we're going to put them out."

The CDC director, however, had been definitive that Covid-19 would still be present in the winter. "We're going to have two viruses circulating at the same," Redfield said at the briefing. Redfield also said that the Post's story quoted him accurately.

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases and a member of the White House coronavirus task force, said later in the briefing that the disease would last beyond the summer.

"We will have coronavirus in the fall," Fauci said. "I am convinced of that."

Trump on Wednesday morning lashed out at CNN, which reported on the Post's interview with Redfield.

"CDC Director was totally misquoted by Fake News @CNN on Covid 19," Trump tweeted.

On Wednesday afternoon, White House press secretary Kayleigh McEnany said on Fox News that she had just spoken with Redfield on the phone and "the mainstream media has been taking him out of context, as they so often do with Trump administration officials."

McEnany added that what Redfield "was trying to" urge Americans to get a flu shot.

"The flu comes back in the fall. Be smart, American people," Redfield meant to say, according to McEnany.

"That's what he was saying. But leave it to CNN and some of the other networks to really take those comments out of context," McEnany said.

-- CNBC's Jacob Pramuk contributed to this report.

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US officials prepare for 'two viruses' next fall: coronavirus and the flu - CNBC