Another variant was also detected in four people arriving from Brazil this week.
Japan's expanded state of emergency over the novel coronavirus pandemic is expected to dent consumer spending by more than 2 trillion yen ($19.3 billion) as the declaration could lift unemployment and cut sales at eateries and retailers, economists said.
Unlike the earlier seven-week emergency Japan had in April and May a year ago, schools, gyms, theaters and shops will stay open.
At least 44 players and staff have nowtested positive to COVID-19.
Suga's announcement comes less than a week after he declared a state of emergency for Tokyo and three nearby prefectures.
Restaurants and bars are requested to close at 8:00pm and authorities want residents to limit unnecessary outings in the evenings.
Record numbers of restaurants declared bankruptcy in Japan in 2020, according to Tokyo Shoko Research, eclipsing the previous high caused by the March 2011 natural disaster and tsunami.
Though less seriously hit by the pandemic than many other countries, Japan has been unable to rein in the virus.
Record infections and the threat of collapse of the hospital system eventually forced his hand.
The areas affected range from central Aichi, an industrial and commercial hub, to Fukuoka in the southwest, and Osaka, which has reported record new cases in recent days along with neighbouring Kyoto and Hyogo prefectures.
Is the state of emergency response too late?
Nagahama said in a report his estimate also reflects the impact of the suspension since December 28 of the "Go To Travel" campaign, a government-subsidized program meant to boost the virus-hit domestic tourism sector.
The state of emergency, Japan's first since April, began first with the greater Tokyo area covered under it.
About 80 per cent said this year's Tokyo Olympics and Paralympics should be cancelled or delayed.
But polls have shown the public's hope for the Games has faded.
The measures of the latest state of emergency are more relaxed compared to those under the previous one, with no punishment for those that fail to comply.
The measures come just over six months before the virus-postponed Tokyo Olympics are due to open.
"The government will work with full force to within a month prevent the spread of infections by all means so that the country will be back to stage 3" of the four-level coronavirus alert level, he said in an interview with The Asahi Shimbun on January 12.
"Person-to-person contact should be thoroughly reduced and the current restrictions on events are loose".