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4 year oldOne plane has landed at a US Air Force air base in California, and its passengers will be isolated at military facilities for 14 days.
There were some 400 Americans on board the Diamond Princess. The ship with some 3,700 passengers and crew has been in quarantine since 3 February.
Meanwhile, China reported a total of 2,048 new cases on Monday.
Of those new cases, 1,933 were from Hubei province, the epicentre of the outbreak.
More than 70,500 people across China have been infected by the virus. In Hubei alone, the official number of cases stands at 58,182, with 1,692 deaths. Most new cases and deaths have been reported in Wuhan, Hubei's largest city.
In other developments:
The cruise ship was put in quarantine in Japan's port of Yokohama after a man who disembarked in Hong Kong was found to have the virus.
On Monday, Japanese officials said there were 99 new cases of infections on board the ship, bringing the total to 454 confirmed cases. It is the largest cluster of cases outside China.
A Russian woman who was on board and tested positive is thought to be the first Russian national to contract the virus after the two previous cases found in Russia were Chinese nationals, Reuters news agency reports.
She will be taken to a hospital for treatment, the Russian embassy in Japan said.
At least 40 US citizens who were on board are infected and will be treated in Japan, Dr Anthony Fauci, Director of the National Institute of Allergy and Infectious Diseases told US broadcaster CBS.
The two aircraft chartered by the US government left Tokyo's Haneda Airport in the early hours of Monday. The second flight was due to land at another base in Texas.
More than 300 passengers are being repatriated voluntarily, the US state department said. Fourteen of them were reported during transit to have tested positive for the virus and were being kept separate from the other passengers, it said.
Those entering the US will undergo a 14-day quarantine, on top of the time they have already spent confined on the ship.
"And the reason for that," Dr Fauci added, "is that the degree of transmissibility, on that cruise ship, is essentially akin to being in a hotspot."
Some of the Americans have declined to be evacuated, preferring to wait until the ship quarantine comes to an end on 19 February.
Passenger Matt Smith, a lawyer, said he would not want to travel on a bus to the plane with possibly infected people.
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