Morang, Sunsari, Jhapa, Kathmandu, Bhaktapur, Lalitpur, Chitwan, Kaski, Rupandehi and Kailali are among the districts with more than 500 active cases of COVID-19 each.
Deuba, the 75-year-old President of the Nepali Congress comfortably won a trust vote in the reinstated lower House of Representatives, averting a general election in Nepal amid the pandemic.
As many as 249 lawmakers participated in the voting process and 83 of them voted against Deuba while one lawmaker remained neutral.
A failure to win the vote of confidence by PM Sher Bahadur Deuba will lead to the dissolution of the House, and elections will be held within six months.
The Kathmandu valley has been under prohibitory orders since April 29 when a devastating wave of COVID-19 was sweeping across the country.
The 75-year-old veteran politician took the oath of office and secrecy from President Bidya Devi Bhandari during a swearing-in ceremony.
Deuba will not take oath as Nepal PM until President Bhandari revises notice of his appointment: Report
A five-member Constitutional Bench led by Chief Justice Cholendra Shumsher Rana, in its order, had said that Deuba must be appointed the Prime Minister in line with Article 76 (5) of the Constitution.
"It is the duty of players to play the game. The referee is there to maintain fair play, not to help any one team to win," Oli said speaking in Nepali language.
The election scheduled for November following the dissolution of the House of Representatives will not be held immediately as the Parliament has been reinstated.
Sher Bahadur Deuba's appointment is in line with the ruling issued by the Supreme Court on Monday to make way for his claim to premiership, replacing incumbent K P Sharma Oli.
Deuba will have to secure the vote of confidence in parliament within a month after his appointment as the new prime minister.
US Ambassador Randy Berry handed over the vaccines to Health Minister Krishna Gopal Shrestha on Monday.
A five-member Constitutional Bench of the Supreme Court on Monday also ordered appointment of Nepali Congress President Sher Bahadur Deuba as prime minister within two days.
Nepal signs USD 1.3 bn mega-deal with Indian company to develop 679 MW Lower Arun Hydropower project
The 679-megawatt Lower Arun Hydropower project is the second mega project undertaken by India after the USD 1.04 billion 900-MW Arun-3 hydroelectric project.
President Bhandari dissolved the lower house for the second time in five months on May 22 and announced snap elections on November 12 and November 19.