How South African Scientists Localized the Omicron Variant

On Friday, November 19, Raquel Viana, director of science at one of South Africa’s largest private testing laboratories, sequenced the genes of eight samples of coronaviruses — and got the biggest shock of her life.

All samples tested at the Lancet laboratory contained large numbers of mutations, especially in the spike protein, which the virus uses to enter human cells.

“I was shocked by what I saw. I wondered if anything had gone wrong in the process,” she told Reuters, an idea that quickly gave way to “a deep feeling that the samples would have huge ramifications.”

She quickly called her colleague at the National Institute of Communicable Diseases (NICD) in Johannesburg, gene sequencer Daniel Amoako.

“I didn’t quite know how to break the news to him,” recalls Viana. “To me it looks like a new strain,” she said to Amoako.

The discovery of the omicron variant in southern Africa has caused global alarm, with other countries limiting travel from that region and imposing other restrictions for fear that it could spread quickly, even in vaccinated populations.

Amoako and his team at the NICD spent the weekend of November 20 and 21 testing the eight samples Viana sent them, which had the same mutations, he said on Tuesday (30).
It was so strange that Amoako, her colleague Josie Everatt, and other scientists also thought it was a mistake. Then they remembered that during the week they had noticed a sharp rise in Covid-19 cases, the kind that could indicate a new mutant.

In addition, Viana had been alerted to a uniqueness in the sample earlier this month by a colleague — a flaw in the S gene, one of the mutations that now distinguishes the new omicron variant of the coronavirus from the one that predominates in the world today, delta.

The only common variant with this trait was alpha, “and we hadn’t seen alpha [na África do Sul] since August,” Everatt says he thought as he tested the samples.

On Tuesday (23), after testing another 32 from the Johannesburg and Pretoria area, “it became clear,” said Amoako. “It was scary.”

​Painful questions

On the same Tuesday, the NICD team informed the Department of Health and other laboratories in South Africa that were doing sequencing, which later began to find similar results.

​On 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.

On November 24, NICD officials and the department notified the WHO (World Health Organization).

At that stage, Viana said, more than two-thirds of the positive tests in Gauteng, the South African province that includes Pretoria and Johannesburg, showed the missing target of the S gene (called a “dropout” in English) — a sign that the micron was already becoming the dominant strain.

Thanks to omicron, the rate of daily infections in South Africa should quadruple, reaching more than 10,000 by the end of this week, according to Salim Abdool Karim, one of the country’s leading experts on infectious diseases, said on Monday (29).

The important questions — what is the new variant’s ability to evade immunity from vaccines or previous disease, how severe the symptoms are compared to previous versions, and how this will differ between age groups — remain unanswered.

Three scientists interviewed by Reuters who are working on these questions expect answers in about three to four weeks.

Meanwhile, South African President Cyril Ramaphosa is considering mandatory vaccination in some contexts, with the country still rocked by 3 million Covid-19 infections and more than 89,000 deaths during the pandemic.

There is a lot of irritation in South Africa over travel bans imposed by other countries — some of them aimed at scientists. Amoako gets some irate messages saying they should “stop looking” for new variants.

Wolfgang Preiser, a virologist at Stellenbosch University who works at Covid-19 and has also received hate mail, fears that other countries might take this whole saga as a lesson not to be too transparent.

“It could encourage other countries to hide things, or just not look at it,” he said. “That’s the fear. Research requires a big investment, so maybe they’ll conclude, ‘We won’t be bothered.'”

_{Translated by Luiz Roberto M. Gonçalves}