How dangerous is the new virus variant from South Africa?

style="float: right; margin-bottom: 10px; font-weight: 600;"Sun 28th Nov, 2021

Is this now the virus variant that is even more contagious than Delta? Or even one that is so different that the vaccine no longer provides sufficient protection and needs to be adapted and updated? To put it bluntly, no one can answer these crucial questions conclusively right now.Still, far too little is known about the Sars-CoV-2 variant B.1.1.529, also known as "Omikron," which was first detected in South Africa. But there is certainly reason for concern, for precautions such as those taken by the United Kingdom, the United States and now Germany, Austria, Italy, the Czech Republic and Malta with restrictions on entry from South Africa. "This newly discovered variant worries us," said Jens Spahn, the still-acting German health minister, on Friday morning. "That's why we are taking proactive and early action here." The last thing missing now, he said, is an "introduced new variant that causes even more problems." Until the restriction takes effect, he called on returnees from South Africa to voluntarily undergo a PCR test and quarantine themselves until the results are in.

The main reason for concern is the amount of mutations in B.1.1.529. In the gene for the S protein alone, the sting with which the virus enters cells, the researchers count 32 mutations, more than twice as many as in the delta variant. However, the sheer number of altered genetic building blocks (compared to the original virus) alone is not the decisive measure. Since the beginning of the pandemic, innumerable virus variants have emerged, counting dozens, hundreds and thousands of mutations, but just as quickly as they arrived, they disappeared again - either because they were no longer viable at all due to the abundance of changes, or because they had no survival advantage over their already circulating relatives, despite good infection and reproduction capabilities.

But in the case of B.1.1.529, some of the 32 mutations are located at positions that researchers have already identified as critically important for the infectivity of viruses, such as positions 655, 679 and 681 in the viral genome. This is the location in the gene blueprint of the S protein where the sting must be trimmed by human enzymes so that the virus can enter the cells.

The better this works, the sooner the virus can multiply, for example, in the upper respiratory tract, where it is more likely to be transmitted to the next person with the next breath or cough. Other mutations probably also contribute to the increased infectivity, for example at positions 203 and 204 in the genome of B.1.1.529, where the blueprint for the "nucleocapsid", the nuclear envelope of the virus, is located.

In addition, B.1.1.529 has some mutations that could enable the viruses to at least partially escape the attack of neutralizing antibodies, such as the immune system of a vaccinated or recovered person sends out to fight: a so-called "immune escape". Structural biologist James Naismith of Oxford University, speaking on a BBC radio program Friday, said he was "almost certain" that existing vaccines protect fewer effectively against B.1.1.529 than against existing variants, such as delta or beta.

South African virologist Shabir Madhi also believes that conventional vaccines provide only limited protection against the new Corona variant B.1.1.529. He told TV station eNCA in Johannesburg on Friday, "We assume that there is still some protection," but it was likely that previous vaccines would be less effective.

"Since the vaccines are efficient against all previous variants, I assume that there is also vaccine protection against this variant," said Richard Neher, an expert in viral evolution at the Biozentrum of the University of Basel, in contrast. Especially the cellular immune response, i.e. not based on antibodies but T cells should be "robust" according to his assessment. "However, it's quite conceivable that breakthrough infections will increase [with B.1.1.529], making the third dose all the more important."

However, these statements are not based on tests with the new South African variant, but on experience with viruses that partly carry mutations similar to B.1.1.529. In laboratory tests with such modified viruses, neutralizing antibodies from the blood of vaccinated or recovered individuals were not as effective as with other coronavirus variants. The absence of a fragment of genetic material in sections 105 to 107 is also thought to contribute to the fact that the viruses are no longer as well recognized and combated by certain defense reactions of the cells, the cellular innate immune system, which may ultimately also contribute to the transmissibility of the viruses.

That linking all these properties to the mutations is not just molecular biology coffee-table talk is shown by the information on the spread of the variant. In the Kwazulu-Natal region, B.1.1.529 is already displacing the delta variant, i.e. it now occurs more frequently than delta in the sequenced samples.Experts are observing something similar in other regions of South Africa and at a breathtaking rate. In the Kwazulu-Natal region, the proportion of B.1,1,529 samples increased from 1 percent frequency to 30 percent in just two weeks. By Thursday, nearly all South African regions were detecting the variant.

It is rather unlikely that this is merely a "founder effect", i.e. the random appearance of this variant in one or more outbreaks and a massive spread emanating from it. While Delta and previous virus mutants took many weeks to become the predominant variant, B.1.1.529 catapulted to the top of the infection statistics within 14 days.

That means, according to initial estimates, B.1.1.529 could have a 500 percent infection advantage over the original variant; Delta has a 70 percent advantage. The variant has also emerged outside South Africa, for example in Hong Kong, introduced by a traveler who infected another person in his hotel, according to investigations by authorities there. Israel has also already reported the case of a passenger arriving from Malawi.

The first B.1.1.529 case in Europe has been detected in Belgium. This was announced by Belgian Health Minister Frank Vendenbroucke on Friday afternoon. Then on Saturday, the Hesse state government let it be known that the variant had reached Germany "with a very high probability." According to Hessian Social Affairs Minister Kai Klose, several mutations typical of the Omikron variant were found in a traveler returning from South Africa the night before. "So there is a high-level suspicion," the Green politician wrote on Twitter. The affected person had been isolated domestically.

The Omikron variant of the coronavirus is also suspected to have occurred in the Czech Republic.Dozens of countries worldwide have sounded the alarm about the new coronavirus variant. Numerous countries decided on Friday to arm themselves against an introduction from southern Africa with extensive flight and entry bans as well as new quarantine regulations. The World Health Organization (WHO) classified the variant as a cause for concern and gave it the name "Omikron".

New virus variant provides sufficient arguments for travel restrictions

There are therefore sufficient arguments for rapid travel restrictions - especially in light of the poor experience with the spread of the delta variant, which failed to be contained, not least because border controls were carried out too late.However, whether the variant also leads to a more aggressive course of the disease, more frequent severe illnesses, and even more deaths, cannot yet be predicted, simply because of a lack of information. The lesson to be learned from experience with Delta, however, is that a much more infectious variant alone increases the incidence of severe disease. Because if more people are infected, more can fall ill.

It is important to emphasize that this variant can still disappear. The absolute number of people infected with B.1.1.529 in South Africa is still low compared to Delta. But the scenario alone in which this variant has now occurred is cause for concern, but it should not surprise anyone: In South Africa, 75 percent of the population is still unvaccinated, in part because of the lack of vaccine there, which rich countries such as the EU continue to fail to provide in sufficient quantities, as the World Health Organization (WHO) has been complaining for months.

This is the breeding ground on which these variants develop because every single infection of a person gives the virus millions of opportunities to generate new mutations as it reproduces. And in South Africa, there are many HIV-infected people whose immune systems are weakened if they cannot take their antiviral drugs regularly. In such immunocompromised patients, the viruses can accumulate more mutations because the body has less to oppose their multiplication, experts suspect.

Scientist Susan Hopkins of Imperial College in London called the new variant "the most worrying we have ever seen." The transmission rate (R-value) detected in South Africa so far is 2, she said, adding that more data are still needed to come to a conclusive assessment. However, a resurgence of infections in a heavily infested country such as South Africa suggests that new variations are at least partly responsible, Hopkins continued. If higher transmissibility proves true, the variant would become "a massive problem."

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