Photo/Illutration An electron microscope image of the Omicron variant of the novel coronavirus (Provided by the National Institute of Infectious Diseases)

The Omicron variant of the novel coronavirus flowed into Japan in four separate forms, and three of them have spread across the country, causing the latest wave of infections, according to a study.

Researchers at the National Institute of Infectious Diseases came up with this theory after analyzing the genome of the virus using samples from 2,650 patients infected with the Omicron variant in Japan.

The samples were obtained through Jan. 17. People who tested positive at quarantine stations were excluded from the study.

The NIID estimated the paths of the virus subvariants in Japan by comparing the small differences in genetic information among them.

The comparisons showed that the Omicron variant (BA. 1 strain), which has wreaked havoc in Japan since mid-December, could be roughly split into at least four groups.

The first subvariant group was found widely in the Kansai region from late December. The genetic information of this group was close to the Omicron variant in Europe.

The research showed that this subvariant has been localized mainly in the Kansai region. Anti-virus measures, such as identifying infected patients at an early stage, helped to contain that subvariant in the region at the end of last year.

But the three other subvariants have spread across Japan.

The second subvariant was genetically close or identical to the virus common in the United States. It was found in some prefectures and then spread throughout the nation.

According to the NIID, this virus subgroup is the most common in Japan and has become “the current mainstream of infections.”

The third Omicron subvariant was initially confirmed in the Kyushu region, but it has also spread widely across Japan. It is genetically close or identical to the virus found in the United States or Britain.

The fourth subgroup was similar to the virus detected in Europe or in other parts of Asia. This subvariant has hit the Kanto and Tohoku regions.

However, the NIID said that detection of the third and fourth Omicron subgroups is currently low.

“A variant can be brought into Japan from abroad or it can occur domestically,” a NIID researcher said. “We need to establish a system to monitor the viruses at the genome level in Japan, including at quarantine stations.”

The NIID said the reach of the variants, like the one in the Kansai region, can be limited if measures are taken in the initial stage.

“It is important to keep infection cases down” after the first discovery of the variant to make it difficult for it to spread further, the NIID said.

The NIID’s findings are available on its website: (

Since mid-December, an increasing number of people who returned from abroad and those in close contact have tested positive for the Omicron variant. More people have since been infected through community transmission in which the infectious source is unknown.

In mid-December, an infection cluster led to hundreds of COVID-19 cases at a U.S. military base in Okinawa Prefecture. Some Japanese workers there were infected with the Omicron variant.