South Africa's Foreign Ministry did not immediately comment. Trump's move was made in conjunction with a new requirement from the Centers for Disease Control and Prevention that all global travellers to the USA obtain a negative test for COVID-19 within three days of boarding their flight. Travelers from Brazil would also be affected.
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The South Africa variant has not been discovered in the United States, but another variant - originating in the United Kingdom - has been detected in several states.
The new requirements go into effect on Tuesday.
The White House on Monday night (South African time) confirmed that new US President Joe Biden had signed the relevant order.
"With the pandemic worsening, and more contagious variants emerging around the world, this is not the time to be lifting restrictions on global travel", she said.
Just over a year after the first US -based coronavirus case was detected, the nation surpassed a harrowing pandemic milestone on Sunday: 25 million confirmed cases, according to data from Johns Hopkins University's Coronavirus Resource Center.
Then-President Donald Trump directed on January 18 those restrictions on Brazil and Europe be lifted effective Tuesday but Biden's proclamation will rescind that decision. But numerous mutations in each variant - eight of those found in the British variant and 10 of those in the South African variant - drew special concern because they sit in the spiky proteins that dot the outside of the coronavirus and have been the key target for vaccines and therapeutics.
Fauci noted that a spike in transmissibility would ultimately lead to more deaths as a result of increased infections and hospitalisations.
Research showed that the vaccine was less effective against the v.5021 strain compared to other variants.
President Joe Biden is set to reinstate Covid-19 travel restrictions on non-US travellers from Brazil, Ireland, the United Kingdom and 26 other European countries that allow travel across open borders.
The 26 European countries impacted by reinstatement of the ban are part of the border-free Schengen zone.
Last week, Mr Biden issued an executive order directing federal agencies to require global air passengers to quarantine upon arrival in the US.
Even with a negative test, returning residents and those travelling from low-risk areas, are advised to self-isolate for at least seven days and submit another sample for testing before venturing out.