Japan experienced the biggest wave of COVID-19 ever in July. With the spread of the more contagious Delta variant, cases have set a record, more than four times the previous wave, with approximately 26,000 cases per day.
A few months after the peak, the number of cases hovers around 140 per day. Scientists know that the rapid increase is due to the Delta variant, but they have not yet fully figured out how cases fell so quickly in countries as other countries continue to fight the virus.
Researchers at Japan’s National Institute of Genetics argue that the Delta variant may have been a victim of its own success. The rapidly mutating species may have mutated itself in Japan, causing it to become extinct. Ituro Inoue and his colleagues believe the virus has acquired a mutation in its error-correcting protein, causing genetic errors to accumulate too much to replicate anymore, the Japan Times reported.
While this is probably not the first time a virus has “self-destructed” under the weight of its own rapid evolution, this event is not often documented and may have been a lucky moment for the nation.
“We were totally shocked by the findings,” Inoue said in an interview with The Japan Times. “The delta variant in Japan was highly contagious and kept out other variants. But as the mutations accumulated, it eventually became a faulty virus and became a virus of its own,” Inoue said. “If we don’t think cases are increasing, we think that at some point during these mutations it headed straight for natural extinction.”
The idea began when the researchers examined the genomic profiles of the Delta variant and compared them to the Alpha variants. What was expected was that the Delta variant was extremely diverse and many lines diverged from the original type. Instead, they discovered that the Delta variant actually only had two large bands before it seemed to stop abruptly. The delta variant, at least in Japan, no longer mutates and splits into subspecies.
The researchers looked more deeply at the viral protein nsp14. This protein has previously been shown to be a proofreading enzyme in RNA viruses – meaning that every time the virus’s genetic code replicates, nsp14 scans the newly created genetic material to make sure no errors are found. Mutations in correction enzymes are catastrophic for organisms that don’t replicate frequently, so for a virus that enters a cell, replicates into thousands of virions, and explodes out of a host cell in about 10 hours, a faulty enzyme is utter disaster.
The researchers found multiple genetic changes in a region within nsp14 called A394V. These mutations seem to contribute to a crippled virus that cannot be replicated. This may explain how the Delta variant disappeared from Japan within a few months.
The theory is certainly interesting, but it doesn’t fully explain why the problematic virus has outstripped the dominant strain. Of course, there are other explanations: Japan has one of the highest vaccination rates and people are extremely disciplined about wearing masks, which means it’s easier to contain epidemics quickly in populated areas.
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