• The identification of a new Covid variant comes as countries scramble to contain two other contagious strains that have emerged in the U.K. and South Africa.
• Public health experts have expressed concern the fresh strains could pose a threat to inoculation efforts.
• In recent weeks, optimism about the mass rollout of coronavirus vaccines appears to have been tempered by the resurgent rate of virus spread worldwide.

LONDON — Japan's National Institute of Infectious Diseases on Sunday said it had detected a new variant of the coronavirus in four travelers arriving from Brazil.

The newly discovered mutant strain of Covid-19 was found to share some of the mutations in common with those of concern for increased infectivity, the institute said, referring to highly infectious variants recently discovered in the U.K. and South Africa.

However, at this time any information about the new variant is limited to its genetic makeup, the NIID said. The institute added it is difficult to immediately determine how infectious the new strain is and the effectiveness of vaccines against it.

The World Health Organization has been contacted by CNBC to confirm whether it has been informed about the new mutant strain of the virus. The United Nations health agency was not immediately available to respond on Monday morning.

The WHO's Director-General Tedros Adhanom Ghebreyesus later said during a press briefing on Monday that the agency had been alerted over the weekend of a new coronavirus mutation found in Japan. He said the new, contagious strains are "highly problematic" if allowed to burden hospitals already under intense pressure.

"The more the virus spreads, the higher the chance of new changes to the virus," Tedros said at the WHO's headquarters in Geneva.

Japan's identification of a new variant of the virus comes as countries scramble to contain two other contagious strains that have emerged in the U.K. and South Africa. Public health experts have expressed concern the fresh variants could pose a threat to inoculation efforts.

To be sure, while the strains discovered in Britain and South Africa spread more easily, there is no clear evidence of the mutated viruses being associated with more severe disease outcomes. But being more transmissible means additional people can get infected, and this could mean more serious infections and added fatalities.

In recent weeks, optimism about the mass rollout of Covid vaccines appears to have been tempered by the resurgent rate of virus spread worldwide.

What do we know about the new variant?

On Jan. 6, Japan's NIID detected a new mutant strain of Covid in four passengers arriving from Brazil's Amazonas state on Jan. 2.

One male in his 40s, who was found to be asymptomatic on his arrival in Japan, was hospitalized as his respiratory condition worsened. One female in her 30s reported a sore throat and headache, one male aged between 10 and 19 recorded a fever and one young woman over the age of 10 was asymptomatic.

The variant of the virus discovered in Japan belongs to the B.1.1.248 strain and has 12 mutations in the spike protein, the NIID said.

Japan's Health Ministry said studies were underway to determine the effectiveness of coronavirus vaccines against the new variant, Reuters reported Sunday, citing an unnamed ministry official.

What about the strains discovered in the UK and South Africa?

On Dec. 14, health authorities in the U.K. reported a variant to the WHO identified as SARS-CoV-2 VOC 202012/01. It is unclear how the new strain originated, but preliminary findings have determined it is highly transmissible.

It initially appeared in southeast England, but within a few weeks, the variant of the virus had already started to replace other virus lineages in some areas of the country.

The U.K. is struggling to contain the spread of the virus, with already stressed health facilities under increasingly intense pressure nationwide. As of Dec. 30, the VOC-202012/01 variant had been reported in 31 other countries and territories worldwide.

Separately, national authorities in South Africa on Dec. 18 announced the detection of variant 501Y.V2. The WHO said routine sequencing showed this strain had largely replaced other SARS-CoV-2 viruses circulating in the Eastern Cape, Western Cape and KwaZulu-Natal provinces by mid-November.

Preliminary studies have shown the 501Y.V2 variant also has increased transmissibility, but there is no clear evidence to suggest it is associated with worse disease outcomes. As of Dec. 30, it had been reported in four other countries.

What is the situation in Japan?

On Thursday Japan declared a state of emergency in the greater Tokyo area after a record number of Covid cases were reported in the country's capital city.

As he announced the new restrictions, Japanese Prime Minister Yoshihide Suga said, "The situation has become increasingly troubling nationwide and we have a strong sense of crisis." He added the measures were necessary to tackle an "increasingly troubling" third wave of infections.

To date, the country has recorded 290,270 cases of the coronavirus, with 3,855 related deaths, according to data compiled by Johns Hopkins University.

— CNBC's Holly Ellyatt contributed to this report.