SARS-CoV-2 coronavirus variant COVID-19 is on the rise in South Africa, and researchers are racing to find out why. Mutations found in other variants, including Delta, appear to be rapidly spreading across South Africa with this variant.
A top priority is to closely monitor the spread of the variant, which was first discovered in Botswana earlier this month and has since been found in a traveller arriving in Hong Kong from South Africa.. The variant’s properties, such as whether it can evade vaccine-induced immune responses and whether it causes more or less severe disease than other variants, are also being studied by scientists.
According to virologist Penny Moore, whose lab is evaluating the variant’s ability to avoid immunity from vaccines and previous infections, “We’re flying at warp speed,” she says in Johannesburg, South Africa. Re-infections and cases in people who have been vaccinated have been reported but “at this stage, it’s too early to tell anything,” says Moore.
Dr. Richard Lessells, an infectious diseases physician at the University of KwaZulu-Natal in Durban, South Africa, said at a press briefing organised by the country’s health department on November 25, “There’s a lot we don’t understand about this variant. It’s a concern, but we need to do the work to understand the significance of this variant and what it means for the pandemic response.”
According to the World Health Organization’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG) on SARS-CoV-2 Variant B.1.1.529 (Omicron), the strain has been designated as a variant of concern and given the name Omicron. Omicron has been added to the current WHO list of variants of concern, joining Delta, Alpha, Beta, and Gamma.
Researchers are also interested in assessing the variant’s ability to spread around the world, which could lead to new outbreaks or amplify the rises currently being driven by Delta.
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Changes to spike
Botswana genome-sequencing data yielded the discovery of B.1.1.529. The spike protein — the SARS-CoV-2 protein that recognises host cells and is the primary target of the body’s immune responses — has more than 30 modifications in this variant. Variants such as Delta and Alpha have been linked to a greater ability to infect and evade infection-blocking antibodies.
South Africa’s Gauteng province, which includes the city of Johannesburg, appears to be experiencing a spike in cases of the variant. According to Lessells, the number of cases in the province surged significantly in November, particularly among students and young people. Researchers at the University of KwaZulu-Natal found that the B.1.1.529 variant was responsible for all 77 of the virus samples they examined from Gauteng between November 12 and November 20, which were collected between November 12 and November 20. Hundreds of additional samples are currently being analysed.
Genotyping tests, which can provide results much more quickly than genome sequencing, can detect the variant because it carries a spike mutation. Preliminary results from these tests indicate that B.1.1.529 has spread far beyond Gauteng. There is concern that this variant is already widely disseminated in the country, according to Lessells.
Researchers will monitor the spread of B.1.1.529 in South Africa and the rest of the world to better understand its dangers. Efforts to study the Beta variant, which was discovered in South Africa in late 2020, have been stepped up, and similar efforts are underway to study B.1.1.529.
B.1.1.529 has already been started by Moore’s team, which provided some of the first data on Beta’s ability to evade immunity. Antibody-blocking antibodies, as well as other immune responses, will be tested to see if the virus can evade the virus. There are many mutations in the spike protein that could reduce the effectiveness of antibodies against it. This evasion is likely being aided by mutations that we don’t yet know about, says Moore. Moore claims that computer modelling suggests that B.1.1.529 may be able to evade the immune protection provided by T cells, another immune system component. First results are expected in two weeks.
Aris Katzourakis, who studies virus evolution at the University of Oxford, UK, says, “A burning question is ‘Does it reduce vaccine effectiveness, because it has so many changes?'” Vaccines from Johnson & Johnson, Pfizer–BioNTech and Oxford–AstraZeneca have all been linked to breakthrough infections in South Africa, according to Moore. It has been reported that the Pfizer vaccine has been administered to two quarantined Hong Kong travellers who have tested positive for the variant. During hotel quarantine, one person was infected; the other had travelled from South Africa.
B.1.1.529 will also be studied in South Africa to see if the disease it causes is more severe or milder than that caused by other B.1.1.529 variants. “The most important question revolves around the severity of the disease.”
B.1.1.529’s threat to the rest of the world is still a mystery, researchers say. Moore also notes that it isn’t clear if COVID-19 is more transmissible than Delta because of the low number of cases in South Africa. This is a quiet time,” she declares. B.1.1.529 should be monitored in countries where Delta is prevalent, according to Katzourakis. Let us see how this virus performs in terms of competitive success and whether it spreads.
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