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The American Medical Association (AMA) called out the Centers for Disease Control and Prevention (CDC) on Wednesday for releasing what it deemed "confusing" and "counterproductive" COVID-19 quarantine and isolation guidance

In a statement, the group's president, Dr. Gerald Harmon, said the American people should be able to count on the agency for timely, accurate and clear guidance. 

Instead, he said, the CDC's new recommendations are "not only confusing, but are risking further spread of the virus."

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"With hundreds of thousands of new cases daily and more than a million positive reported cases on January 3, tens of thousands – potentially hundreds of thousands of people – could return to work and school infectious if they follow the CDC’s new guidance on ending isolation after five days without a negative test," Harmon said. "Physicians are concerned that these recommendations put our patients at risk and could further overwhelm our health care system."

He said that negative tests should be required for ending isolation after a positive test, adding that reemerging without knowing one's status "unnecessarily risks further transmission of the virus."

"Test availability remains a challenge in many parts of the country, including in hospitals, and we urge the administration to pull all available levers to ramp up production and distribution of tests. But a dearth of tests at the moment does not justify omitting a testing requirement to exit a now shortened isolation," he concluded. 

Registered nurse Emily Yu, left, talks to Paul Altamirano, a 50-year-old COVID-19 patient, at Providence Holy Cross Medical Center in Los Angeles, Dec. 13, 2021.

Registered nurse Emily Yu, left, talks to Paul Altamirano, a 50-year-old COVID-19 patient, at Providence Holy Cross Medical Center in Los Angeles, Dec. 13, 2021. (AP Photo/Jae C. Hong, File)

Ahead of the new year, the CDC announced that it would shorten its recommended isolation and quarantine period from 10 to five days.

"People with COVID-19 should isolate for five days and if they are asymptomatic or their symptoms are resolving (without fever for 24 hours), follow that by five days of wearing a mask when around others to minimize the risk of infecting people they encounter," it said in a statement. 

In addition, the CDC said people exposed to COVID-19 who are unvaccinated or are more than six months out from their second mRNA dose – or more than two months after the Johnson & Johnson vaccine – and not yet boosted are recommended to quarantine for five days followed by strict mask use for an additional five days. 

Individuals who have received their booster shot do not need to quarantine following exposure but are advised to wear a mask for 10 days after the exposure.  

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For all exposed, best practices would include a test for SARS-CoV-2 at day five after exposure, and individuals should immediately quarantine if symptoms occur until testing negative.

While the CDC was criticized over the guidance, CDC Director Dr. Rochelle Walensky defended the decision – saying that previous guidance had been "conservative."

"The change is motivated by science demonstrating that the majority of SARS-CoV-2 transmission occurs early in the course of illness, generally in the 1-2 days prior to onset of symptoms and the 2-3 days after," the CDC wrote in its guidance.

On Tuesday, the CDC updated its protocol for ending isolation, saying Americans can take a COVID-19 test toward the end of the five-day isolation period if they have "access." 

Dr. Rochelle Walensky, director of the Centers for Disease Control, testifies before the Senate Health, Education, Labor, and Pensions Committee about the response to the ongoing COVID-19 pandemic in the Dirksen Senate Office Building on Capitol Hill on Thursday, Nov. 4, 2021, in Washington, D.C.

Dr. Rochelle Walensky, director of the Centers for Disease Control, testifies before the Senate Health, Education, Labor, and Pensions Committee about the response to the ongoing COVID-19 pandemic in the Dirksen Senate Office Building on Capitol Hill on Thursday, Nov. 4, 2021, in Washington, D.C.  (Kent Nishimura / Los Angeles Times via Getty Images)

The agency said that tests "are best used early in the course of illness to diagnose COVID-19" and are not authorized to "evaluate duration of infectiousness."

"Data, including a review of 113 studies from 17 countries, show that most SARS-CoV-2 transmission occurs early in the course of infection," the CDC wrote in its explanation. 

While White House Press Secretary Jen Psaki said the CDC's decisions were led by science, external factors, like keeping the labor force operational, were also a factor, according to Walensky.

"There are a lot of studies [from other variants] that show the maximum transmissibility is in those first five days," Walensky said. "And [with omicron] we are about to face hundreds of thousands more cases a day, and it was becoming very, very clear from the health care system that we would have people who were [positive but] asymptomatic and not able to work, and that was a harbinger of what was going to come in all other essential functions of society."

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All of this comes as the omicron variant of the coronavirus continues to spread around the country, leading to staffing shortages in multiple fields and an increase in pediatric hospitalizations, with more than 95% of new COVID-19 cases linked to the variant of concern.

Although scientists recognize that the variant is more transmissible than other COVID-19 strains, more research is being done to determine its severity of disease and ability to evade immune response and vaccines – as well as the future of the pandemic in the U.S.

Fox News' Paul Best contributed to this report.