What's different about the hyper-infectious delta coronavirus variant?

TOKYO -- Coronavirus infection numbers are exploding, and severe cases are hitting record highs in Japan. The prime suspect in the surge is the virus's delta variant, now estimated to account for over 90% of the country's COVID-19 cases. Delta is apparently vastly more transmissible than its predecessor strains, and more likely to lead to serious symptoms. What exactly is different about this strain compared to the original virus?

"It's one of the most transmissible viruses we know about," Centers for Disease Control and Prevention (CDC) Director Rochelle Walensky said of the delta variant in a CNN interview. According to an internal CDC document reported by The Washington Post, the delta variant's basic reproduction number, the average number of people that each infected person is expected to infect, is estimated at five to 9.5. It is also believed to be drastically more infectious than severe acute respiratory syndrome (SARS) and seasonal influenza. Walensky said the delta variant is even as transmissible as chickenpox.

In Japan, daily new coronavirus infections topped 20,000 for the first time on Aug. 13. The number of cases doubled in less than a month from July 29, when daily new infections exceeded 10,000, and cases have continued to surge. It is highly likely that the delta variant, which has been rapidly replacing the conventional COVID-19 strain on a global scale, is a factor behind the sudden rise in nationwide cases.

Why is the delta variant so infectious? Many experts have taken note of the L452R mutation, which is a change in the "spike protein" on the surface of the virus which attaches to human cell receptors upon infection. It appears that the spike protein mutation has increased its ability to bind to cells.

In an L452R mutation, the 452nd amino acid in the spike protein is replaced from leucine to arginine. Kobe University professor Shigenori Tanaka specializes in quantum life science and conducts spike protein analysis using the Japanese supercomputer Fugaku, developed by the government-backed Riken research institute. He pointed out that the mutation is a "significantly dangerous one that intensifies the virus strain's transmissibility."

Infections with the delta variant may have also raised the risk of developing severe symptoms. In Japan, there has been a noticeable increase in hospitalization of patients in their 40s and 50s, an age group previously resistant to serious COVID-19.

Japan's health ministry has also presented findings that symptoms including a fever and cough are more likely to arise after getting infected with the delta than the alpha variant. There is also the possibility that increased amounts of virus particles in the body is connected with severe symptoms.

The delta variant itself also mutates frequently, creating a string of new sub-lineages. Among these are mutations that could apparently be more likely to evade antibodies acquired through vaccination, as well as to cause viral proliferation. Experts have been closely monitoring the mutations.

The delta variant is classified into smaller groups, based on differences in the DNA sequences examined through whole viral genome sequencing. Sub-lineages point to strains deriving from the delta variant which have mutated even further.

Sub-lineages and variant strains may be classified as "variants of interest" (VOI) or "variants of concern" (VOC) by the World Health Organization (WHO), considering how they spread, and are assigned Greek letters, like alpha or delta.

Hiroaki Takeuchi, associate professor at Tokyo Medical and Dental University, commented, "If it's a mutation that is convenient for the virus, it's possible that it will multiply more efficiently within the body." As the delta variant also has a mutation that has made it easier for it to bind to cells, Takeuchi said that "it is thought that the virus' overall power will be enhanced, and there is no denying that it has also become more transmissible."

Another important factor is that if there are many infections, there are also more opportunities for mutation, making it easier for new variants to appear. With more people acquiring immunity through vaccination, virus variants that evade this immunity could also become rampant. Current vaccines were not designed to counter the delta variant, and any decline in the shots' preventative powers versus delta is not now clear.

Jun Ohashi, population genetics professor at the University of Tokyo, said, "Although the improvement of vaccines in line with mutations is not technically difficult, we risk falling into a negative cycle of vaccine rollouts failing to keep pace with the speed of mutations, leading to the failure to curb infections. On the move to administer third "booster shots" of COVID-19 vaccines, which has been spreading in the United States and Europe, Ohashi said, "It's desirable to get vaccines that target variant strains, but if supplies won't make it in time, we have no choice but to use existing vaccines."

What should we do to lower the risks brought by new mutations?

So Nakagawa, a genomics lecturer at Tokai University School of Medicine, emphasized, "Now that the delta variant has spread over such a wide area, it has become necessary to watch out for mutations deriving from this variant. It is essential to keep a close eye on whether distinctive mutations are spreading in specific regions, including countries that have made progress with their inoculations."

Furthermore, the lambda coronavirus variant was detected in Japan for the first time in July, and there is a good chance that new variant strains other than delta will emerge. Nakagawa said, "It's imperative to take measures, including building an infection prevention system by finding new variant strains as soon as possible, by conducting as many virus genome analyses as we can, among other means."

(Japanese original by Ayumu Iwasaki and Ryo Watanabe, Science & Environment News Department)