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Inside SA leg of Omicron variant discovery: A single test result, a missing gene, and an email

In early November, junior scientist Alicia Vermeulen, who works at a Lancet Laboratories facility in Pretoria, spotted something peculiar in the results from a batch of coronavirus testing. She had no idea that her observation would put in motion a sequence of events that would finally result in the revelation that the Omicron coronavirus variety was present and circulating in South Africa, triggering worldwide panic and travel restrictions targeting southern African nations.See the source image

The existence of the B1.1.529 variant - dubbed Omicron on Friday - was confirmed for the first time on 25 November by South African scientist Professor Tulio de Oliveira. However, the first samples were sequenced in Botswana and Hong Kong as early as 11 and 13 November by the Botswana-Harvard AIDS Institute Partnership. The Hong Kong instance included a confined man who came home on 11 November after a 23 October trip to South Africa.See the source image

According to News24, data were submitted to a worldwide repository called GISAID within hours of one another on 22 November and were subsequently picked up by a virologist at Imperial College, London, named Tom Peacock, who shared his discoveries on GitHub and Twitter. By Wednesday, it had been picked up by a British news site.

However, on the afternoon of 4 November, Vermeulen noticed an irregularity in one of the lab's around 300 positive test results that day. She had witnessed something similar earlier this year. The test failed to detect a key gene that is required to identify the presence of the SARS-Cov-2 virus in a sample, the S-gene - which encodes the spike protein.See the source image

Two more genes were discovered in the sample, indicating that it may be categorized as positive. However, the absence of the S-gene indicated that something had changed. This is referred to as "S-gene fallout" or "S-Gene Target Failure" in official parlance. Omicron has a high mutation rate, more than 30, and concerning alterations in the spike protein, which raised first concerns about its ability to evade vaccine-induced immunity.

Although researchers are optimistic that existing vaccinations will continue to protect against severe sickness and death, News24 reported on Saturday that full answers to these critical issues about Omicron might take "weeks."


Inside SA leg of Omicron variant discovery: A single test result, a missing gene, and an email | News24

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Alicia Vermeulen Hong Kong Lancet Laboratories Omicron Pretoria


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