'Was Quite Shocked at What I was Seeing': South African Scientist on Discovery of Omicron Variant

The WHO has warned of the potential for Covid surges with severe consequences fueled by omicron, whose constellation of mutations suggests it may be both more transmissible and capable of evading the immunity provided by vaccination or prior infection.

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New Delhi: While processing Covid-19 tests in early November, laboratories in South African provinces began picking up something unusual and weren't able to detect the virus gene easily, said reports. However, on Friday, November 19, Raquel Viana, Head of Science at one of South Africa's biggest private testing labs, got the shock of her life when she sequenced the genes on eight coronavirus samples as all bore a large number of mutations, especially on the spike protein that the virus uses to enter human cells and spreads.

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During a conversation with news agency Reuters, Viana said, "I was quite shocked at what I was seeing. I questioned whether something had gone wrong in the process." She added that it was "a sinking feeling that the samples were going to have huge ramifications".

Explaining the order, she said how she quickly contacted her colleague at the National Institute for Communicable Diseases (NICD) in Johannesburg, gene sequencer Daniel Amoako and discussed about it. "I didn't quite know how to break it to them," she recalls. She told Amoako, "To me, it looks like a new lineage."

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    Later that weekend (November 20-21), Amoako and the team at the NICD spent their time testing the eight samples which Viana sent them, all of which had the same mutations. While testing the samples, Amoako, his colleague Josie Everatt and other colleagues gave it a thought that it must be a mistake, but then they remembered that over the week, they had noticed a sharp rise in COVID-19 cases, of the sort that might indicate a new mutant. In addition, Viana had been alerted to an oddity in the sample earlier this month by a colleague - an S-gene dropout, one of the mutations that now distinguishes the new Omicron variant of the coronavirus from the globally dominant Delta one, added the Reuters report.

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    The only common variant with that feature was Alpha, "and we hadn't seen Alpha (in South Africa) since August," Everatt recalls thinking as they tested the samples. And, by Tuesday (November 23), after testing another 32 samples from around Johannesburg and Pretoria, "it was clear," Amoako said. "It was scary", he added.

    The NICD team then informed the department of health and other labs across South Africa doing sequencing, which later started coming up with similar results. The same day, the NICD entered the data into the GISAID global science database and found that Botswana and Hong Kong had also reported cases with the same gene sequence. And, on Wednesday (November 24), NICD officials and the department notified the World Health Organisation (WHO).

    The WHO has warned of the potential for Covid surges with "severe consequences" fueled by omicron, whose constellation of mutations suggests it may be both "more transmissible" and capable of evading the immunity provided by vaccination or prior infection. The emergence of the Omicron variant in southern Africa has caused global alarm, with countries limiting travel from the region and imposing other restrictions for fear it could spread quickly even in vaccinated populations.

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    Published Date:December 1, 2021 2:24 PM IST

    Updated Date:December 1, 2021 2:28 PM IST