The Japan Times
How serious are new COVID subvariants?
In the third year of the COVID-19 pandemic, there is no shortage of new coronavirus variants to track.
On April 11, Japan reported its first case of the omicron XE variant, in a woman who arrived at Narita Airport from the U.S. That was followed by news on May 2 that a man in his 50s who flew to Haneda Airport from the U.S. was also infected with XE. Also, on April 28, a previously unknown omicron variant was reported in a patient in the city of Sendai.
So what are these variants? Why do new variants keep emerging? And how alarmed should we be? Here’s what you need to know about the current situation regarding coronavirus variants.
What is the dominant coronavirus variant currently circulating, both in Japan and globally?
Currently, the dominant type is the omicron variant. It was first detected in South Africa in November and quickly replaced the delta variant, which had been driving infections worldwide. Delta, first detected in India in late 2020 and found in a patient in Japan in April 2021, had itself overtaken the alpha variant, which emerged in Britain in fall 2020.
Viruses constantly evolve and mutate, changing their genetic code while replicating inside our cells. Omicron is a heavily mutated strain of the original form of the coronavirus that spread in Wuhan, China, in late 2019 — there are 30 mutations in the spike protein, which is the part of the virus that binds to a cell receptor to gain entry. Preliminary data suggests that symptoms caused by omicron may be milder than those of previous variants, although some people may still develop severe disease and could die.
Omicron, the standard form, or sublineage, of which is known as BA.1, has spawned a slew of subvariants — such as BA.2, which is currently the dominant sublineage in many countries including Japan, as well as BA.4 and BA.5, which have recently taken hold in South Africa. Meanwhile in the U.S., the sublineage BA.2.12.1 has spread rapidly since mid-March, accounting for 36.5% of all newly sequenced cases in the week ending April 30, according to the Centers for Disease Control and Prevention.
Hiroaki Takeuchi, associate professor of virology at Tokyo Medical and Dental University, has carried out genome sequencing of omicron variants in patients at the
university’s affiliated hospital. He described the virus variants as being in a “constant tug of war” with each other.
“The variants that won the battles have survived,” he said. “A virus’s strength or weakness is determined by its infectiousness, which is its ability to infect the host and replicate inside the body, and its transmissibility, which is its ability to transmit itself to other people. That’s why we have seen newer variants that emerged as winners cause larger waves of infections.”
What are the differences between BA.1 and BA.2?
Both of these are sublineages of the omicron variant of the coronavirus, but there are some differences in the amino acids in their spike protein and other proteins. BA.2 is believed to be more transmissible than BA.1, with a higher effective reproduction number — the average number of cases generated by an infected person — and a shorter generation time, which is the time between the start of an infection in one person and the start of infection in someone else that person infected.
According to the World Health Organization’s February statement on BA.2, which examined clinical data in South Africa, Britain and Denmark, there was no reported difference in severity between BA.1 and BA.2.
What kind of variants are the XE variant and the one found in Sendai?
These variants are both “recombinant viruses” or “recombinant variants.” A recombinant virus occurs when someone is infected with two or more variants at the same time, causing the genetic material of those viruses to mix in their body.
Various recombinant lineages have been found and assigned names starting with X and a letter, such as XA, XB and XC, although most of them have not spread widely enough to become a public health concern. Of the many omicron recombinant variants, XE — which contains the genetic information of BA.1 and BA.2 — spreads about 10% faster than BA.2, but its chance of causing severe illness seems not to be much higher than BA.2, experts say.
More than 1,500 cases of XE have been confirmed globally since it was first detected in Britain in January, according to the health ministry. Japan has not reported any cases apart from the two that were detected during airport screening.
The new variant found recently in Sendai is also an omicron recombinant, but it features a mix of BA.1 and BA.2 in the spike protein, unlike previously reported omicron recombinants in which the spike proteins come from either sublineage but not both, according to Tomoya Saito, director of the Center for Emergency Preparedness and Response at the National Institute of Infectious Diseases. He said there is no data yet on how infectious and virulent this variant is, but considering no other cases have been found, there is no reason to be overly worried at this point.
Are we going to see more variants appear?
Probably. For example, Takeuchi said he recently detected a subtly new version of BA.2 in two of 116 patients whose virus genomes were sequenced by his team while they were being treated at the hospital for COVID-19.
The virus had a mutation called L452M, indicating a change in the chain of amino acids that form the spike protein. The delta variant and the BA2.12.1 omicron subvariant both feature a mutation in the same position of the spike protein, but with different amino acids, Takeuchi said, raising concern that this new virus from the BA.2 subvariant family may fuel new infections in Japan.
But in general, viruses become less damaging to humans through a process of adaptation, where they learn how to coexist with their hosts — humans — for their survival, Takeuchi said.
“The coronavirus will likely reduce its damage to hosts, because they cannot survive if it becomes highly pathogenic and kills too many,” he said. “Omicron has shown that it tends not to cause severe symptoms compared with previous variants. This is largely because we have more weapons at hand, like vaccines and anti-coronavirus drugs, but I think we will come across variants that find a balance to live alongside humans.”
The classification system for variants has also recently become more refined, making it possible for scientists to define subtle differences, said Takeuchi.
“Before, we used to define mutated viruses broadly, like alpha and delta,” he said. “But since the emergence of the delta variant, scientists have started to assign separate names to subtly different versions of the same variant. So you might think the coronavirus has undergone huge changes, but that’s not the case.”
What measures should citizens and the government take over the new variants?
Takeuchi said booster shots of the COVID-19 vaccines, which are based on the genomic sequence of the original coronavirus strain, will continue to be effective in keeping those infected from developing severe symptoms.
He also said mask-wearing should remain in place in Japan, at least for the next one or two years, until the nation is fully prepared for future spikes in infections thanks to domestically developed vaccines and sufficient testing kits and oral medication for everyone who needs them. In terms of what the government needs to do, he stressed the importance of creating a system where the country can produce its own vaccines and oral medication without relying on imports.
“I think we will see another pandemic within the next 10 years,” Takeuchi said. “It might be a coronavirus variant or a whole new pathogen, but a system where we can develop and provide our (own) vaccines and anti-pathogen drugs would be crucial. I think that’s the biggest lesson to be learned from the pain Japan has suffered this time.”