Vexing and volatile variants of the coronavirus are adding fuel to the fire as Japan braces for its fourth and possibly largest wave of the pandemic.

Tokyo, Kyoto and Okinawa on Monday joined a growing list of prefectures that have imposed a fresh set of countermeasures to fend off a viral rebound inflamed by new strains of the coronavirus that are more contagious and harder to detect.

A significant increase in testing for COVID-19 — and genomic screening for its variants — would better reveal where and to what extent the mutant contagion is spreading, and allow public officials to respond accordingly, but experts question the country’s willingness and ability to do so.

Without that, they said, variants spreading unseen could propel the outbreak to record-breaking heights.

“Japan’s testing for the coronavirus has always been lacking, and the same can be said now of its attempt to detect variants,” said Hiroshi Kasanuki, a visiting professor at Waseda University’s Medical Regulatory Science Institute. “Disjointed attempts to screen for variants across different regions speaks to the absence of a cohesive, nationwide policy.”

Currently, public officials are screening for variants by selectively analyzing polymerase chain reaction (PCR) tests that were positive for COVID-19.

While the scope and methodology used to conduct PCR tests differs across towns, cities and prefectures, the way tests are screened for variants seems to vary even more.

Furthermore, PCR tests don’t always detect variants, and genomic sequencing or blood analysis provides more reliable screening.

In Osaka, the N501Y variant, which first emerged in the United Kingdom late last year, remains the most common mutant form of the virus . In Tokyo, however, a different variant — the E484K variant, which has been widely reported in Brazil and South Africa — accounts for a majority of variants detected in screened cases.

In Osaka, public officials are mostly screening for variants among COVID-19 patients linked to cluster infections. In Tokyo, where screening methods are less defined, cases are significantly lower despite having a significantly larger population.

“We’re screening for variants on a case by case basis,” a Tokyo official said Wednesday.

People cross a street in Shinjuku Ward in Tokyo on Tuesday. | REUTERS
People cross a street in Shinjuku Ward in Tokyo on Tuesday. | REUTERS

Differences in testing methods could explain the widening divide in new cases between the two major cities.

In total, variants have been detected in more than 1,000 cases in Japan. Nearly 400 were found to be of the E484K variant, most of which were concentrated in the Kanto region surrounding the capital.

Since late December, the Tokyo Metropolitan Government has screened roughly 4,700 positive PCR tests, of which 195 — or about 4% — were found to involve variants.

Among test results that have undergone genomic screening, variants have overtaken the original coronavirus strain in a handful of prefectures.

Of the strains detected by the metropolitan government between March 29 and April 4, the N501Y variant accounted for about 32%, while isolated E484K variants accounted for nearly 42%. The original coronavirus strain accounted for the remaining 26%.

While there’s still much to be learned about new strains of the coronavirus, even less is known about the E484K variant. Scientists fear isolated forms of it may be more contagious than other variants and that existing vaccines may be less effective in guarding against it.

The strain first detected in the U.K. — which consists of the isolated N501Y variant — is thought to be 75% more contagious and 1.6 times more fatal. The South African and Brazilian strains contain both the N501Y and E484K variants and are thought to be more contagious, but it’s unknown how much more fatal.

Tokyo officials don’t yet know whether the isolated E484K variant, which is emerging in an increasing number of cases in the capital, is either more contagious or fatal.

Meanwhile, Tokyo is aiming to strengthen its testing capacity in preparation for a sharp uptick that could surpass the country’s third wave of infections.

As of late March, about 10% of coronavirus cases in the city were being screened for variants. Earlier this month, the Tokyo Metropolitan Government announced it would raise that figure to 25% by the first half of April and eventually to 40% as quickly as possible.

“A majority of residents won’t receive a vaccine while new measures are in effect,” Tokyo Gov. Yuriko Koike told reporters Monday. “We’re fighting the variant barehanded.”

Variants account for a growing portion of new cases in Osaka, Tokyo and Hyogo, among other prefectures, but low testing is most likely concealing the true scope of the spread of mutated strains.

Including the results of genome analysis conducted by the central government, as of Thursday the capital had reported 195 cases involving variants. Despite the difference in population size, Osaka Prefecture has detected variants in more than 200 cases, and Hyogo Prefecture nearly 200. Tokyo has a population of nearly 14 million, while Osaka is home to 8.8 million and Hyogo just under 5.5 million.

The number of tests conducted may be a factor. In early April, Tokyo was conducting just under 7,000 PCR tests a day, whereas Osaka was conducting more than 10,000 a day throughout much of the same period.

A COVID-19 rebound was expected after major cities began to reopen in early March, but perhaps not this soon or in so many parts of the country. And certainly not with the added confusion caused by mutated forms of the coronavirus.

COVID-19 vaccinations for people age 65 and over started Monday at the Hachioji Municipal Government building in Tokyo. | POOL / VIA KYODO
COVID-19 vaccinations for people age 65 and over started Monday at the Hachioji Municipal Government building in Tokyo. | POOL / VIA KYODO

Meanwhile, Japan began to vaccinate the elderly in more than 39 prefectures Monday.

The country aims to inoculate more than 36 million people age 65 and older by the end of June, but it’s unclear how effective existing vaccines are in eradicating mutated forms of the coronavirus.

On Sunday, a hospital staffer in Ishikawa Prefecture tested positive for COVID-19 after receiving both doses of Pfizer Inc.’s vaccine.

“The central government will work with local governments so the vaccination of the general population will begin as soon as possible,” Chief Cabinet Secretary Katsunobu Kato said during a news conference Monday.

Japan may have had an opportunity to extinguish these puzzling variants when they first emerged months ago.

Variants were first reported in Japan in late December among a group of travelers that had just returned from a trip to the U.K.

The mutated strains began to proliferate in Kobe and Sendai soon after that. In Kobe, variants were found in half of its screened PCR tests as early as February.

“That was when the country needed to form a national response to what was clearly inevitable,” Kasanuki said. “And now there’s no choice but to try and contain this mutating outbreak through increased testing and aggressive contact tracing.”

The N501Y variant has been detected in cases across the U.K., South Africa and Brazil, but only in South Africa and Brazil have they been found to be mixed with the E484K variant.

In Japan, an abrupt surge spearheaded by more contagious variants of the virus could overwhelm hospitals and force officials to implement more restrictions on economic activity and public movement.

According to a simulation released by the Tokyo Metropolitan Government, the capital could surpass 1,000 cases a day by April 22 if new infections grow weekly by 50%, by mid-May if they increase by 20% and by mid-June if they grow by 10%.

Researchers at the University of Tokyo predicted that the economic fallout of a fourth wave propelled by variants could triple or quadruple that of a state of emergency without variants. The countermeasures needed to contain variants, they said, would demand stricter measures that further stall economic activity.

A growing list of prefectures are falling back under restrictive measures just weeks after the central government began lifting the country’s second state of emergency, which had been declared in as many as 11 prefectures to stem a third wave that began in early January.

'New cases are emerging at an increasing rate in the capital,' warned Tokyo Gov. Yuriko Koike during a meeting at the Tokyo Metropolitan Government building on Thursday. | RYUSEI TAKAHASHI
‘New cases are emerging at an increasing rate in the capital,’ warned Tokyo Gov. Yuriko Koike during a meeting at the Tokyo Metropolitan Government building on Thursday. | RYUSEI TAKAHASHI

New restrictions were imposed in Osaka, Miyagi and Hyogo prefectures earlier this month and took effect on Monday in Tokyo, Kyoto and Okinawa.

These measures, which were made possible by the revision of the country’s infectious disease laws in February, allow prefectural governors to request that local businesses close early and urge residents to stay indoors for a fixed period of time, in specific parts of their prefectures.

Dining establishments have been asked to close by 8 p.m. — an hour earlier than previously requested — until May 5 in the cities of Osaka and Sendai, as well as in Kobe and Hyogo’s Amagasaki, Nishinomiya and Ashiya.

The same restrictions took effect Monday in Tokyo’s 23 wards as well as six cities located in its western Tama region, and will last until May 11. They will be enforced until May 5 in the city of Kyoto as well as nine cities in Okinawa Prefecture, including Naha.

Critics say it’s unlikely these new measures — which are intended to prevent the need for a state of emergency and are therefore less restrictive — will be able to contain a fourth wave, seeing as new cases began to grow while stronger measures were in place during the state of emergency.

“Securing hospitals for coronavirus patients is the priority, but PCR tests should be administered to as many people as possible and those who test positive should be isolated immediately,” said Mitsuyoshi Urashima, chief of the Jikei University School of Medicine’s Division of Molecular Epidemiology. “Otherwise, asymptomatic carriers will continue to spread the virus and variants will accelerate the process.”

The N501Y variant began to wreak havoc in England in December, when it grew to account for 60% of new infections, provoking a wave that went on to trigger thousands of new cases and overwhelm hospitals in Wales and London, despite an ongoing lockdown in the British capital.

Experts fear that Tokyo, with two variants of varying volatility spreading quickly, could follow the same path.

“The worst case scenario is a repeat of London here in the Japanese capital,” Urashima said. “We need to prevent that.”

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