As the world continues to reel from the devastating Covid-19 pandemic, which is completing its two-year run on the planet, the panic button is being pressed again with the surfacing of newly discovered B.1.1.529 strain. Declared by the World Health Organisation (WHO) a variant of concern and renamed Omicron, it has been blamed for a surge in fresh cases in South Africa, but has already cropped up in Hong Kong, Belgium, Israel, Botswana, The Netherlands, Australia and Denmark. The classification puts Omicron into the most-troubling category of Covid-19 variants, along with the globally-dominant Delta, plus its weaker rivals Alpha, Beta and Gamma.
Nations rushed to ban flights to slow the spread of Omicron, while stock markets and oil prices plunged on fears surrounding the variant, potentially dealing a heavy blow to the global economic recovery. Researchers in South Africa are racing to track the evolution of the new variant of the Sars-CoV-2 coronavirus that causes Covid-19. A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveller arriving in Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do.
“We’re flying at warp speed,” says Penny Moore, a virologist at the University of the Witwatersrand in Johannesburg, South Africa, whose lab is gauging the variant’s potential to dodge immunity from vaccines and previous infections. There are anecdotal reports of reinfections and of cases in vaccinated individuals, but “at this stage it’s too early to tell anything”, Moore adds.
Researchers spotted Omicron in genome-sequencing data from Botswana. The variant stood out because it contains more than 30 changes to the spike protein — the Sars-CoV-2 protein that recognises host cells and is the main target of the body’s immune responses. Many of the changes have been found in variants such as Delta and Alpha, and are linked to heightened infectivity and the ability to evade infection-blocking antibodies. The variant harbours a spike mutation that allows it to be detected by genotyping tests that deliver results much more rapidly than genome sequencing does.
To understand the threat Omicron poses, researchers will be closely tracking its spread in South Africa and beyond. Researchers in South Africa mobilised efforts to quickly study the Beta variant, identified there in late 2020, and a similar effort is starting to study Omicron. Moore’s team — which provided some of the first data on Beta’s ability to dodge immunity — has already begun work on Omicron. They plan to test the virus’s ability to evade infection-blocking antibodies, as well as other immune responses. The variant harbours a high number of mutations in regions of the spike protein that antibodies recognise, potentially dampening their potency. There are even hints from computer modelling that Omicron could dodge immunity conferred by another component of the immune system called T cells, says Moore. Her team hopes to have its first results in two weeks.
“A burning question is ‘does it reduce vaccine effectiveness, because it has so many changes?’,” says Aris Katzourakis, who studies virus evolution at the University of Oxford, UK. Moore says breakthrough infections have been reported in South Africa among people who have received any of the three kinds of vaccines in use there, from Johnson & Johnson, Pfizer-BioNTech and Oxford-AstraZeneca. Worrying times indeed.
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