The Nikkei average dropped 2.53% to 28,751.62, its lowest finish since Oct. 25, and posting its biggest daily fall in more than five months. The broader Topix fell 2.01% to a six-week closing low of 1,984.98.
For the week, the Nikkei lost 3.3%, while the Topix fell 2.9%, marking the biggest decline since the last week of September.
“The market’s fundamentals have been weak as investors kept selling when the Nikkei got closer to 30,000,” said Kazuharu Konishi, head of equities at Mitsubishi UFJ Kokusai Asset management.
“So, it easily got damaged by negative news, such as the one about the new virus variant. Although it might be too rough to conclude that today’s declines were only due to the virus.”
The variant, detected in South Africa, may be able to evade immune responses and has prompted Britain to hurriedly introduce travel restrictions on South Africa.
The news hit travel-related shares, which had been benefiting from a surge in domestic consumption due to successful containment of the virus, the hardest.
Topix airline shares index dropped 5.4% to a seven-month low while Topix land transport index, made up mainly of train operators, lost 2.9% to a one-year low.
ANA Holdings fell 4.5% after the airliner raised funds through a sale of convertible bonds, a move that highlighted the difficulty facing the industry.
Among railway operators, Keisei Electric Railway fell 6.3% to become the worst performer in the Nikkei.
Central Japan railway lost 3.3%, while Western Japan Railway shed 3.2%.
Softbank Group tumbled 5.2% after Bloomberg reported Chinese regulators have asked top executives of ride hailing giant Didi Global to devise a plan to delist from the New York Stock Exchange due to concerns about data security.
The Japanese conglomerate is a large investor in U.S.-listed Chinese tech firms, including Didi and Alibaba.