The delta variant drove a record number of nearly 26,000 daily cases in Japan, and three months later, new COVID-19 infections have fallen in Japan, dropping below 200 in recent weeks. Additionally, no deaths were reported on November 7, something that had not occurred in approximately 15 months.
But why is this happening? Why did the fifth and largest wave of coronavirus in Japan – carried out by the supercontagious delta variant with an increase in cases – come to an end so abruptly? Did Japan do something different from other developed countries that are experiencing new cases to the contrary?
According to a group of researchers, possibly this is due to the fact that the delta variant in an act of taking care of itself caused its “self-extinction”, after undergoing many mutations during its evolution.
Academics point to a variety of possibilities. On the one hand, there is the vaccine. Among advanced countries, Japan has one of the highest vaccination rates: as of Wednesday, November 17, 75.7 percent of residents were vaccinated with the full schedule. And on the other side is social distancing and mask-wearing measures, which are now deeply ingrained in Japanese society.
However, the main reason may be related to the genetic changes that the coronavirus undergoes during its reproduction, at a rate of approximately two mutations per month, reports The Japan Times.
According to a theory proposed by Ituro Inoue, a professor at the National Institute of Genetics, the delta variant in Japan accumulated too many mutations in the non-structural protein called nsp14, responsible for the correction of errors of the virus. So the virus struggled to fix the bugs in time and was led to “self-destruction” as a result.
Studies have shown that, compared to people in Europe and Africa, there are more in Asia that have a defense enzyme called APOBEC3A, which attacks RNA viruses such as SARS-CoV-2 (the one that causes COVID-19).
For this reason, researchers from the National Institute of Genetics and the University of Niigata decided to discover how the APOBEC3A protein affects the protein. nsp14 and if it can inhibit the activity of the coronavirus.
So what the team did was an analysis of the genetic diversity data, this with clinical samples infected between June and October with the alpha and delta variants within Japan.
To show genetic diversity, the researchers used a diagram called a haplotype network, where they looked at the relationship between the DNA sequences of the SARS-CoV-2 virus. In general, the larger the network, the more positive cases it represents.
The alpha variant network, which was the main driver of Japan’s fourth wave from March to June, had five main clusters with many mutations branching out, confirming a high level of genetic diversity.
And in the case of the delta variant – which according to Centers for Disease Control and Prevention it is more than twice as contagious as previous variants, being capable of causing more serious disease in unvaccinated people — it was thought to have much more vibrant genetic diversity.
But surprisingly, the opposite happened. The haplotype network had only two main groups and mutations seemed to stop suddenly in the middle of their evolutionary development process.
When the researchers moved on to examining the error-correcting enzyme nsp14 of the virus, they found that the vast majority of nsp14 in Japan they seemed to have undergone many genetic changes at mutation sites called A394V.
“The delta variant in Japan was highly transmissible and it kept other variants out. But as the mutations accumulated, we think it eventually became a defective virus and was unable to make copies of itself. Taking into account that the cases have not increased, we believe that at some point during such mutations it went directly towards its natural extinction, “said Inoue.
The rest of the world has similarly high vaccination rates and is experiencing record waves of new infections, but Japan appears to be a case in point, in that COVID-19 cases have remained subdued despite trains and Restaurants get crowded in there.
That is why Inoue’s theory could support the disappearance of the spread of the delta variant in Japan. “If the virus were alive and healthy, the cases would surely increase, since the mask and vaccination do not prevent breakthrough infections in some cases,” said the researcher.
According to Inoue, a similar natural extinction of the coronavirus may be observed abroad. However, this would be somewhat difficult to detect, since no other country seems to have accumulated so many mutations in the nsp14 virus as in Japan, despite the fact that similar mutations have been found in at least 24 countries at the site A394V.