Japan’s fifth wave of Covid-19 has virtually disappeared so dramatically that some scientists are puzzled as to why it happened. One team suggests the highly infectious Delta strain mutated into extinction on the island nation.

In mid-August, Japan experienced a peak in Covid-19 infections, recording over 23,000 new cases per day. Now the metric is just around 170, with deaths attributed to the disease mostly remaining in single digits this month.

The decline has been attributed by many to high vaccination rates, public acceptance of masks, and other factors, but some researchers say the drop was uniquely significant, compared to other nations with similar conditions.

Ituro Inoue, a geneticist at the National Institute of Genetics, believes that Japan had the good fortune of witnessing the Delta strain mostly rooting out other variants of the SARS-CoV-2 virus before then eradicating itself. He explained his team’s theory to the Japan Times newspaper this week.

For some time now, Inoue and his fellow scientists were researching mutations of SARS-CoV-2 and how they are affected by the protein nsp14, which is crucial for the reproduction of the virus.

RNA viruses, like the one causing Covid-19, tend to have a very high mutation rate, which helps them quickly adapt to changes in the environment. However, this opens the door for a so-called “error catastrophe,” when bad mutations pile up and finally cause the full extinction of a strain. The protein nsp14 appears to offer a form of error proofreading that helps the virus genome to stay below the threshold of the “error catastrophe.”

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In the case of Japan’s fifth wave of Covid-19, the Delta variant’s nsp14 failed at this job, Inoue believes, based on the genetic study of specimens collected from June to October. Contrary to his team’s expectations, there was a lack of genetic diversity, while many samples had many genetic changes in the site called A394V, which is linked to the error-fixing protein.

“We were literally shocked to see the findings,” the researcher told the Japan Times. “The Delta variant in Japan was highly transmissible and [was] keeping other variants out. But as the mutations piled up, we believe it eventually became a faulty virus and it was unable to make copies of itself.”

The theory could be relevant to the previous SARS strain, which was identified in 2003, explaining why it didn’t cause a pandemic. But that would be hard to confirm, since the outbreak ended relatively quickly and didn’t result in the massive collection of genetic data necessary to test the hypothesis.

It’s not clear why Japan had this lucky turn of events, but nothing comparable happened in other East Asian countries like South Korea, where populations are genetically close to that of Japan. Virus mutations similar to those flagged by the scientists have been discovered in at least 24 countries, Inoue said. He and his team plan to publish a paper detailing their findings by the end of November.

Even if the natural extinction theory is confirmed, it is at best a temporary reprieve for the Japanese people. New, more successful strains are likely to eventually find their way into the country, though quarantine measures and immigration control could delay the emergence of new variants in Japan, Inoue believes.

Meanwhile, Tokyo is bracing for a new wave of Covid-19 this winter and is preparing to live with the virus. The government reportedly plans to ease travel restrictions by increasing the number of people it allows to enter the country per day from 3,500 to 5,000.

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When The Washington Post reported this week that CIA Director William Burns slipped into Afghanistan on Monday to meet with Taliban leader Abdul Ghani Baradar, it was described as the highest-level face-to-face encounter between the Taliban and the Biden Administration.  WaPo cited anonymous sources for the information and the CIA offered no immediate comment on the reporting.  If the reporting is accurate, it doesn’t answer any immediate questions about why the President would dispatch the CIA director for such a meeting.

What we do know, is that the unexpected advances of the Taliban that have dominated the headlines over the past week and a half were initially blamed on an intelligence failure by many.  Early on, Cipher Brief Expert and former Acting Director of CIA John McLaughlin tweeted that “The ‘intelligence failure’ drumbeat is starting. People should be careful about the charge if they have not actually seen/read the intelligence…”

So, what intelligence did the US have that would have led to a different outcome in Kabul and throughout the country?

  • The New York Times reported last week that “classified assessments by American spy agencies over the summer painted an increasingly grim picture of the prospect of a Taliban takeover of Afghanistan and warned of the rapid collapse of the Afghan military, even as President Biden and his advisers said publicly that was unlikely to happen as quickly.” The paper cited current and former US government officials, saying, “By July, many intelligence reports grew pessimistic, questioning whether Afghan security forces would muster serious resistance and whether the government could hold on in Kabul, the capital.”
  • On August 15, The Wall Street Journal reported that administration officials said they knew that a “total capitulation of the Taliban was a possibility, and they planned their withdrawal efforts accordingly.” But they also cited an administration official, saying “it wasn’t so much a failure in intelligence in which the administration based its decision, but rather, a change in circumstances brought about by the swift U.S. withdrawal.”

But private sector analysts were watching as well. Here’s an inside look at what The Cipher Brief has been publishing since January with key outtakes from Cipher Brief Expert Tim Willasey-Wilsey:

Brief: January 25, 2021

“The Afghans themselves are also monitoring the Washington newsfeeds in forensic detail and will be encouraged by Sullivan’s statement. Recently, all too many conversations in Kabul have been about when to leave and which route to take. Some wealthier Afghans already have their money in Dubai and children in foreign universities. Some even have passports and property in the United States, UK or Germany. For those who are less fortunate, the discussions are about which route to take out. The Uzbekistan border is favoured because a visa costs just $30 and there is a variety of onward routes via Turkey or Russia to the West whereas the routes via Iran or Pakistan are more restrictive or liable to interference.”

Brief: March 11, 2021

“Saleh will advise Ghani not to take Taliban or Pakistani promises on trust. Instead, Ghani may decide to call Washington’s bluff. He may doubt that Washington is really willing to abandon Afghanistan on 1st May with the risk of a rapid Taliban victory jeopardising all the hard-won advances in areas such as women’s rights and counterterrorism over the past 20 years. The spectre of Al Qaida re-establishing camps in Afghanistan would surely be too much for Biden and Blinken.”

“Even if there were no helicopters from the US Embassy roof, the TV pictures of the Taliban entering Kabul, and of Afghan refugees fleeing their advance could evoke memories of Saigon in 1975. The reimposition of Taliban curbs on women would provoke international opprobrium. And subsequent reports of AQ training camps being re-established in Afghanistan would bring back recent and painful memories. After all the blood and treasure expended in Afghanistan that would be a disastrous outcome.”

Brief: April 19, 2021

“The Afghan government may be able to hold on to power for a few years as the Najibullah administration survived after the Soviet departure. However, there is a danger that there will be a sudden dam-burst in confidence with senior officials and politicians leaving en masse and hundreds of thousands of refugees fleeing westwards through Iran, Pakistan and the Central Asian Republics. As the Taliban re-enter Kabul, we could see disturbing scenes of retribution and, in time, the return of Al Qa’ida figures from their hiding-places in the tribal borderlands in Pakistan. Only then will people re-examine this decision and recognise that the Afghan deployments since 2014 have not been that onerous.”


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Brief: June 1, 2021

“According to my sources, the Taliban are convinced they can take Kabul “within days” of the NATO withdrawal and they believe the Afghan army is “in a shambles and demoralised”. Although the Taliban will not disrupt departing US troops (unless attacked) they are not willing to wait until September to continue their campaign against Kabul government forces.”

“But we should not take much comfort from the Najibullah example. The comparisons with today’s Afghanistan are misleading. Najibullah’s government was able to reach and supply all the major towns by military convoy. The Afghan army was deployed to protect towns and road communications. By contrast, in 2021, only the route between Kabul and Jalalabad is reasonably safe. Convoys cannot get through from Kabul to Kandahar, Kandahar to Herat, or Kabul to Mazar-e-Sharif. The Afghan army is spread across the country in piecemeal district centres (often surrounded by Taliban-controlled countryside) and have to be resupplied by air. This is not a sustainable model.”

“Furthermore, a number of today’s Afghan leaders, officials and military officers have received offers to relocate to the United States, Germany and elsewhere. As the security situation continues to deteriorate, the gradual trickle of departures is likely to gather pace. In such circumstances, the government could implode quite suddenly.”

“To some, this may evoke images of the 1975 fall of Saigon with the big losers being the Afghans who remain, particularly the women, who face a future of uncertainty and anxiety. There could also be a migration crisis reminiscent of Syria in the last decade.”

Brief: June 28, 2021

“One key indicator is that Afghan security forces have begun to surrender to the Taliban. The procedure is quick and simple. Tribal elders are used to deliver a stark message to Afghan troops often holding positions in district centres. The message is often; “The non-believers are leaving Afghanistan. They are defeated. Your leaders are corrupt. You can surrender now, and we will protect you; or you can fight, and we will kill you.” Recently, the Taliban appear to have honoured their promise not to punish Afghan soldiers who surrender. News of this new-found leniency is likely to encourage other units to follow suit and lay down their arms. In several provinces, including in the north, the Taliban are tightening their grip on those cities which are still held by the government. The Taliban will soon be in a position to cut off food supplies and demand their surrender, possibly offering a similarly lenient dispensation to the population. Now that the Taliban possesses captured armoured vehicles and artillery, their ability to exert pressure on the cities is enhanced. In Kabul, a sense of panic has begun to grip the capital. There are desperate attempts to sell family homes but there are no buyers even when houses are on the market at one tenth of their previous value. Some families have departed to Tajikistan, conscious that several of the land border crossing-points with the Central Asian Republics have been captured by Taliban forces in recent weeks.”

Read also Putin’s Calculated Afghanistan Play from Cipher Brief Expert Robert Dannenberg


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