A new virus variant is infecting millions in India. What could its spread mean for Japan?

A potentially more transmissible variant of the coronavirus first identified in India has been fanning record daily tallies there of around 380,000 cases and 3,500 deaths as dozens of countries offer vaccine supplies to help the country of 1.4 billion deal with the growing crisis.

But what do we really know about the new Indian variant? And, as the virus spreads rapidly in Japan, what are the overall ramifications beyond India’s borders?

Found in Japan

The Indian variant, called B.1.617, has several sublineages. One sublineage named B.1.617.3 was first detected in the country in October. What is driving the current second wave of infections in the country, however, are B.1.617.1 and B.1.617.2, both discovered in India in December.

The Japanese government announced last Monday that it has so far detected a total 21 cases of the Indian variant, including 20 cases confirmed via airport quarantine. A woman in her 80s in Tokyo who has been identified as being infected with the variant was released from hospital on April 14, the metropolitan government has said, adding that her travel history remained unclear.

A “double mutant” variant indicates two genetic changes in the spike protein that the coronavirus uses to infect human cells. Adding to concern about this latest variant, however, is that India has discovered a “triple mutant variant” as well.

Thousands of mutations of the coronavirus have been reported around the world. The World Health Organization has branded the Indian variant as one of seven SARS-CoV-2 variants of interest (VOI), which features genetic markers associated with changes to receptor binding and reduced neutralization by antibodies generated by vaccinations. The WHO lists three variants, those first detected in the U.K., South Africa and Brazil, as variants of concern for existing evidence of their increased transmissibility and more severe cases of the disease, including causing more deaths.

The Indian variant is said to be responsible for some 60% of the new cases in some parts of the South Asian country and has been identified in at least 17 countries.

Three mutations

The Indian variant has three characteristic mutations called L452R, P681R, and E484Q.

“L452R has been associated with increased transmissibility, a reduction in neutralization by some (but not all) monoclonal antibody treatments, and a moderate reduction in neutralization in post-vaccination sera in the USA,” WHO said in its weekly COVID-19 epidemiological update last week.

What is even more worrying for Japan is that researchers from Tokyo University and others belonging to the Genotype to Phenotype Japan (G2P-Japan) consortium have found that the L452R variant found in California can bypass HLA-24-restricted cellular immunity. HLA stands for human leukocyte antigen, and scientists say that roughly 60% of Japanese and about 20% of Caucasians in the U.S. have that type of white blood corpuscle. If the discovery holds up — it has not been peer-reviewed — then the majority of Japanese could be susceptible to increased infection risk from the Indian or California variant, which has been spreading fast in the western U.S. state that is home to large numbers of Asian Americans.

“Notably, the L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication,” G2P-Japan said in a summary article on the preprint biology server bioRxiv. “Our data suggest that the HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes, and the escape from cellular immunity can be a further threat of the SARS-CoV-2 pandemic.”

Still, Ugur Sahin, CEO of Germany’s BioNTech SE, which partnered with U.S. pharmaceutical giant Pfizer Inc. to develop an mRNA coronavirus vaccine, said last week that he’s confident that its shot is effective against the Indian variant.

“We are evaluating (the strain) … and the data will be available in the coming weeks,” he told U.S. network CNBC.

X-factor?

Some scientists, including Shinya Yamanaka, a Nobel Prize winner in Physiology or Medicine and Kyoto University professor, have speculated the existence of an X-factor behind the mysteriously low COVID-19 infection rate in Japan and other East Asian countries such as China, South Korea and Taiwan. A higher rate of using masks outdoors and genetic and immunological characteristics have often been cited as possible reasons.

But given the explosive rise in daily infections and deaths in India, some experts are bracing for the possibility that the Indian variant could some day replace the U.K. and other variants in Japan as the top new coronavirus threat due to its unique ability to evade immunity.

These fears have been compounded by the difficulty in detecting the variant.

The National Institute of Infectious Diseases said the lack of an N501Y mutation in the Indian variant, which are common in the variants first detected in the U.K., South Africa and Brazil, makes it impossible to detect via polymerase chain reaction (PCR) tests and that, at the moment, it can only be identified through virus genome testing.