Tuesday, January 31

The new omicron variant puts Europe on guard


The World Health Organization (WHO), meeting to analyze this emerging variant, named it omicron –The fifteenth letter of the Greek alphabet– and warned that it could carry a “higher risk of reinfection”. He classified it as “of concern”, as it “has a large number of mutations, some of which are worrisome.”

The WHO points out that the omicron variant “has a large number of mutations, some of which are worrisome”


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This variant was first reported to WHO from South Africa on November 24, while the first confirmed infection on record came from a sample collected on November 9.

In recent weeks, infections have increased considerably, coinciding with the detection of the B.1.1.529 variant. The number of cases of this variant seems to be increasing in almost all the provinces of South Africa ”, explained the WHO yesterday.

In just two weeks, dozens of cases have already been detected not only in South Africa, but also in neighboring Botswana, Hong Kong and Belgium, a woman who was not vaccinated and who returned from a trip to Egypt 15 days ago. The Hong Kong cases were vaccinated. At the moment there are no cases detected in Spain.

Concern about the new variant B.1.1.529 was triggered in the last hours of Thursday by a thread on Twitter by scientist Tulio de Oliveira, director of the Center for Epidemic Response and Innovation in South Africa. Its tone is reminiscent of a catastrophic Hollywood movie: called on the world to support South Africa “to protect the whole world” and called on “billionaires and financial institutions” for this effort. He even mentioned Bill Gates, Jeff Bezos, Elon Musk and Warren Buffet to read his almost desperate message.

De Oliveira reports that this new variant B.1.1.529, “Very worrying at the mutational level”, has become dominant in the country in less than a week “after a devastating delta wave in South Africa”: it already accounts for 75% of the sequenced genomes and will soon reach 100%, according to their calculations. In the South African province of Gauteng – whose capital is Johannesburg, a city of more than 6 million inhabitants – it accounts for 90% of cases. “We work day and night to understand the effects on transmissibility, vaccines, reinfection, the severity of the disease and the diagnosis,” says the scientist. We have funds for science, but South Africa and Africa need financial help to support their disadvantaged population and health system ”, claims De Oliveira, who is requesting international funding because the South African population cannot endure harsh confinement without aid.

This variant has been detected at a faster rate than previous waves of infection, suggesting that it may have a growth advantage.


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Is there a reason for the alarm? Virologists, immunologists, and biostatisticians agree that this variant needs to be monitored very closely.But they emphasize that there is no need to panic and that there is no way we can go back to the starting point of early 2020. There may be some vaccine leakage or, rather, erosion of the immunity that vaccines produce, but these they will remain largely effective in preventing serious illness and death.

COVID-19 Victims Memorial in London. EFE


The Spanish immunologist Matilde Cañelles yesterday commented on Oliveira’s thread, that described as “quite alarmist”. “The variant contains many mutations in the spike protein (the one used for RNA and DNA vaccines), which could potentially evade the immune response generated by vaccine or by disease with previous variants.” He clarified that these are “very few cases” detected so far, and that “in South Africa there were very few cases of delta in the beginning, which is why it is easier for a variant to predominate”. This is what scientists call the “founder effect.” In addition, as we are in the initial days after its detection, it is unknown if the rapid advance of this variant is due to biological improvements that give it greater transmissibility or to an event of superpropagation, as the University geneticist has repeatedly recalled. scored by Santiago Antonio Salas when we have the information. That is why South African scientists are subjecting the virus to various experiments.

Preliminary evidence suggests an increased risk of reinfection with this variant, compared to others that are also of concern


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Of the total number of mutations of this new variant, 32 (more than double the maximum detected so far), nine appear in other variants of concern. Another mutation of concern is E484K, present in lineages B.1.351 (formerly South African variant, beta) and P.1 (gamma, which caused an epidemic wave in Manaus, Brazil) and associated with immunity evasion. “It has an unprecedented sampling of previously seen mutations in alpha, beta, gamma and delta separately.”, says Jeffrey Barret, head of COVID-19 genomics at the Wellcome Sanger Institute (United Kingdom), on Twitter. “Beyond changes in protein S, there are two mutations in the nucleocapsid, R203K and G204R, which are key to increasing transmissibility, and are present in all variants of concern so far,” adds Barret. He acknowledges that “the mutation profile is bad”, but points out that it is not known how these mutations act together, or how a virus with so many changes will behave. To verify this, the scientists will use other modified viruses to carry the spike protein (S) of this variant and will test whether the serum of those vaccinated, loaded with neutralizing antibodies, works well. Later experiments will test the real virus against these sera.

However, the molecular biologist and journalist of ‘Science’ Kai Kupferschmidt recalls that “our immune system has more than neutralizing antibodies, so none of this tells us how much this variant of immunity will escape and if it will mainly affect protection against infections or also against serious illness ”. The immune response induced by anti-COVID vaccines includes non-neutralizing antibodies and also T cells capable of recognizing many more areas of protein S than those that have mutated. “Although the antibody response may be lost, we have other armies, T lymphocytes, which can do their job, even if the S protein changes,” Africa González, professor of Immunology at the University of Vigo, told TVE yesterday.

A failure of the S gene target in this lineage allows PCR to be used as a marker for the variant before confirmation by sequencing.


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“Given all we know at this stage, I would be very surprised if current mRNA vaccines do not continue to offer robust protection against serious illness and death from B.1.1.529,” biologist Carl T. Bergstrom said on Twitter. theorist and evolutionary and professor at the University of Washington in Seattle (USA). “All effective vaccines, we still do not know if the mutations are affecting the immune response and if they protect 100%, it will always be much better to be vaccinated than not ”, González agrees.

Another of the data that has transpired, that the new variant is up to 500% more transmissible, has not been verified and has been questioned by some experts.

The reason why this variant has emerged in South Africa may have to do, according to some scientists, with the high prevalence of HIV (the virus that causes AIDS) in this African country, which causes a part of the population to have its weakened immune system. Thus, SARS-CoV-2 can remain in the body for months and have time to evolve and develop a high number of mutations.

Poor vaccination

The low vaccination rate in South Africa has also not helped, with only 23.8% of its population using the full schedule, a percentage that is much lower in Africa as a whole: around 7%. This has allowed an increase of 300% in the incidence in the African country in one week. “We should bring vaccines to developing countries, we are all at risk if third world countries are at risk; if not, the variants will come to us, as we are already seeing ”, emphasizes Africa González, who supports the use of“ all means so that there is no extension like the Indian variant, which has affected all countries ”.

One of the good news about this variant is its rapid detection and the commendable transparency with which the South African authorities have transmitted the information to the rest of the world. Another advantage is that it is easy to detect with PCR before going through the longer and more sophisticated process of genomic sequencing. It is because it contains the deletion at positions 69/70 of protein S, just like the British variant (B.1.1.7 or alpha). Almost a year ago now, PCR tests indicating that absence pointed to suspected cases of the British variant. Now the same procedure could be used.




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