Last season, the CDC estimated at least 26 million people suffered from the flu.
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The outbreak has also sickened 17 people and resulted in 13 hospitalizations across 13 states.
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The rollout of free N95 masks for the public began this week across the United States, with some pharmacies already handing out the masks and others expecting to do so in the coming days.
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The American Academy of Pediatrics released new Covid-19 guidance for schools on Monday that supports in-person learning.
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This is the CDC's first public accounting of breakthrough cases, and the agency is searching for patterns based on patient age and gender, location, type of vaccine, variants and other factors.
CDC Director Dr. Rochelle Walensky declined to provide information for the 10% of Americans who are vaccinated and looking for guidance on whether it is safe for them to travel.
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The comments from Fauci come as the US Covid-19 death toll approaches 500,000 and the country nears a full year in its fight against the virus.
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That doesn't mean they should stop taking precautions, the CDC noted in updated guidance. It's just not necessary for them to quarantine.
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The order goes into effect at 11:59 p.m. Monday.
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CDC Director Dr. Robert Redfield is expected to sign the order on Tuesday and it will go into effect on January 26.