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Heavily mutated Omicron variant puts scientists on alert

Researchers are racing to see if a fast-spreading coronavirus variant poses a danger to the efficacy of COVID vaccinations.
Researchers in South Africa are scrambling to find out why a new version of the SARS-CoV-2 coronavirus, which produces COVID-19, is causing such alarm. The variant contains several of the changes reported in other variants, including Delta, and it appears to be rapidly spreading throughout South Africa.

One of the key priorities is to keep a closer eye on the variant as it spreads: it was initially discovered in Botswana earlier this month and has subsequently been found in a visitor coming in Hong Kong from South Africa. Scientists are also trying to figure out whether the variant can avoid immune responses elicited by vaccines and whether it causes more or less severe disease than other variants.

Reinfections and cases in vaccinated people have been reported anecdotally, but it's too early to say anything at this point.

There's a lot about this variety that we don't know. We are concerned by the mutation profile, but we must now try to understand the importance of this variant and what it signifies for the pandemic response, says scientists.

On the suggestion of scientists from the WHO's Technical Advisory Group on SARS-CoV-2 Virus Evolution, the World Health Organization (WHO) identified the strain, known as B.1.1.529, as a variation of concern and called it Omicron on November 26. On the current WHO list of variations of concern, Omicron joins Delta, Alpha, Beta, and Gamma.

Researchers also want to see if the variety has the capacity to spread internationally, potentially causing new waves of infection or increasing Delta's current surges.

B.1.1.529 was discovered in Botswana's genome-sequencing data. The variant stood out because it contains more than 30 modifications to the spike protein, which detects host cells and is the major target of the body's immunological reactions. Many of the alterations have been discovered in Delta and Alpha variants and have been connected to increased infectivity and the ability to elude infection-blocking antibodies.

The apparent significant increase in cases of the variation in South Africa's Gauteng region, which includes Johannesburg, is also raising concerns. In November, the number of cases in the province skyrocketed, especially in schools and among young people. The B.1.1.529 variant was revealed to be responsible for all 77 virus samples collected between November 12 and November 20 in Gauteng, according to genome sequencing and other genetic studies. Hundreds of other samples are being analysed.

A spike mutation in the variation permits it to be discovered by genotyping assays, which provide results considerably faster than genome sequencing. According to preliminary information from these tests, B.1.1.529 has expanded well beyond Gauteng. This raises our suspicions that this variety is already circulating widely in the country.

Researchers will actively monitor B.1.1.529's expansion in South Africa and elsewhere to better understand the harm it poses. Researchers in South Africa deployed resources to immediately investigate the Beta variant, which was discovered there in late 2020, and a similar effort is underway to investigate B.1.1.529.

The goal is to see how well the virus can resist infection-blocking antibodies and other immune responses. The variant contains a significant number of mutations in antibody-recognition areas of the spike protein, potentially reducing antibody efficacy.

Many mutations are known to be harmful, but many more appear to be leading to greater evasion. Computer modelling even suggests that B.1.1.529 could avoid immunity conferred by T cells, another component of the immune system. It is hoped that the first results will be available in two weeks.

'Does it limit vaccine effectiveness because there are so many changes?' is a pressing question.

In South Africa, persons who received any of the three types of vaccinations in use there, from Johnson & Johnson, Pfizer–BioNTech, and Oxford–AstraZeneca, have developed breakthrough infections. Two quarantined travellers in Hong Kong were given the Pfizer vaccine after testing positive for the variation. One person had travelled from South Africa, while the other had became infected while being quarantined in a hotel.

South African researchers will also investigate if B.1.1.529 produces disease that is more severe or mild than other forms. The main question revolves around the severity of the ailment.

According to academics, the threat posed by B.1.1.529 outside of South Africa is yet unclear. Because there are currently few COVID-19 instances in South Africa, it's also uncertain whether the variant is more transmissible than Delta. We've hit a stalemate. Countries with a high prevalence of Delta should be on the lookout for B.1.1.529. We'll have to wait and watch how this virus performs in terms of competitive success and whether it spreads.

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