The domestic outbreak in China had been brought largely under control through strict lockdowns that were imposed early this year - but a new outbreak has been linked to a meat and vegetable market in south Beijing.
The National Health Commission (NHC) said 36 of the new cases were domestic infections in the capital.
The other two domestic infections reported today were in northeastern Liaoning province, and local health officials said they were close contacts of the Beijing cases.
The alert was sounded after the NHC confirmed the first cases in Beijing for two months on Friday and city officials delayed the return of students in primary schools that had not already resumed classes.
Several of the new cases were linked to the Xinfadi wholesale market, and more cases connected with the market emerged yesterday after wider testing.
The market was closed and AFP reporters saw hundreds of police officers - many wearing masks and gloves - and dozens of paramilitary police deployed there yesterday.
The new cluster of domestic infections has prompted fresh lockdowns with people ordered to stay home in 11 residential estates near to the market.
Worries have also grown about the safety of the food supply chain, with some other markets in the city also closed.
State-run media had reported that the virus was detected on chopping boards used to handle imported salmon, and that major supermarket chains had removed stocks of salmon.
Beijing’s market supervision authorities ordered a city-wide food safety inspection focusing on fresh and frozen meat, poultry and fish in supermarkets, warehouses and catering services.
Nine nearby schools and kindergartens have been closed, sporting events, group dining and cross-provincial tour groups have also been stopped.
The majority of cases in recent months have been overseas nationals tested as they return home, and the rest of the cases reported today were imported cases from abroad.