Three days before the Olympics began, on July 20, Japan’s National Institute of Infectious Diseases (NIID) reported to an international organization that the highly infectious Lambda variant had been detected in an airport test in Japan for the first time, but did not announce it widely to the public.
The report was submitted to an international COVID-19 and other influenza virus database known as GISAID. According to preliminary reports from South American and Japanese scientists, the Lambda variant may possess an increased resistance to vaccines. Although scientific data on the variant is limited in comparison to prevalent COVID-19 variants like Delta, its detection in the airport comes at a time when infections in the country are skyrocketing. On Friday, the total number of confirmed COVID-19 cases in Japan passed 1 million and the arrival of Lambda can further complicate matters. For the time being, there appears to have been only one confirmed case.
The Japanese government would not release details, but a researcher at the NIID told The Daily Beast that the variant was found at an airport check and not in the wild. The source said there was a plan to announce the variant’s detection but not until after the Olympics.
The NIID employee said new variant discoveries have previously been announced within three days, if they are well-known variants, but it can take up to 11 days. This year, on Jan. 2, four travelers from Brazil tested positive for the coronavirus. After lab analysis, the Ministry of Health determined that it was a new variant and made an announcement on Jan. 10, a Sunday. Typically, the Minister of Health has a press conference when a major new variant is discovered in Japan for the first time. In December, a Japanese woman who arrived in Haneda Airport after visiting Britain was judged negative after an airport screening. She later became ill and was tested on Dec. 19, and found to be positive for the virus. After determining that it was a British variant, the health ministry announced it eight days later, on Dec. 27.
Government officials had not been willing to tell The Daily Beast when the original Lambda variant test was carried out, but it is now 17 days since they told GISAID about the discovery.
After discovering the Lambda report on the GISAID website on Wednesday, The Daily Beast approached the Ministry of Health, the NIID, and publicly requested information. The ministry initially stonewalled and then told us to wait for a call back with further information on Friday before slipping out the announcement of the case to the state broadcaster. NHK reported the news without mentioning the long, unexplained delay.
Last month, a team of researchers at Tokyo University released a report, not yet peer-reviewed, that found the Lambda variant was highly infectious and displays detectable resistance to immunity acquired by vaccines. In Peru, where the variant was first discovered, more than 90 percent of infections are now traced to the Lambda variant. The research team at Tokyo University believes the variant “has potential to be a threat to human society.”
Japan’s NIID reported finding the Lambda variant to the GISAID database on July 20. The database shared the first complete genome sequence of SARS-Cov-2 in early January 2020 and there have been nearly 2.5 million submissions logged since. Institutes submitting data to the group must have their credentials confirmed and sign a database access agreement.
The variant was confirmed by the SARS-CoV-2 testing team at NIID in Tokyo and the data submitted by the Pathogen Genomics Center at the same institute. Nozumu Hanaoka, a senior research scientist at the institute’s Center for Infectious Disease Risk Management, and several other scientists signed off on the submission. According to GISAID’s Aug. 4 updated transmission tracking data, the variant is believed to have been brought to Japan by an infected patient traveling through the United States.
The woman in her 30s traveled from Peru to Japan’s Haneda International Airport on July 20 where she tested positive for the variant, according to sources close to the Health Ministry, who said the NIID ran tests and confirmed it was the Lambda variant the same day.
There are reportedly no direct scheduled flights from Peru to Haneda or Narita International Airport in Tokyo, with passengers usually making two or more stops in the United States. Travellers from Peru often route through Los Angeles International Airport, California, John F. Kennedy International Airport, New York, or Seattle-Tacoma International Airport, Washington, before making their final departure to Tokyo.
The NIID has not yet responded to requests for further information about the discovery of the variant. For example, was it brought to Japan by a participant in the Olympics? Where was the carrier of the virus quarantined?
An employee of the NIID who spoke to The Daily Beast on conditions of anonymity said, “I’m not authorized to speak on the record but to my knowledge the variant was detected at an airport checkpoint and has not been in the wild [exposed to the general populace].” The employee said that normally when a new variant is found, the information is promulgated quickly, but not this time. “There was a consensus at the Ministry of Health that this information would best be reported after the Olympics were over. Whether that is because they felt that it would be better to heighten public awareness when the news cycle slows down or whether this is because it might tangentially be associated with the Olympics, which is embarrassing—that I don’t know.”
A representative from the Ministry of Health told The Daily Beast that the Lambda variant has not “arrived” in Japan, as it was detected and quarantined at an airport circa July 20. “This means the proper testing protocols work,” they said.
The representative elaborated that there is limited scientific information on how contagious, how viral, and how responsive to vaccines the Lambda variant is.
“We are always monitoring the spread and behavior of variants. However, due to limited data, it is hard to say how dangerous the Lambda variant is. For this same reason, it is difficult to compare it to the Delta variant.”
Kei Sato, a virology researcher at the University of Tokyo, one of the co-authors of the paper “SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance,” confirmed to The Daily Beast that he was aware of a case of the Lambda variant being reported in Japan, but said he was not privy to further details.