On Friday, November 19, Raquel Viana, science director at one of South Africa’s largest private testing laboratories, sequenced the genes in eight coronavirus samples and received the shock of her life.
The samples, analyzed in the Lancet laboratory, had a large number of mutations, especially in the spike protein that the virus uses to enter human cells.
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“I was quite surprised by what I was seeing. I wondered if anything had gone wrong in the process, “he told Reuters, a thought that quickly gave way to” a sinking feeling that the samples were going to have huge ramifications. ”
He quickly picked up the phone from his colleague at the National Institute for Communicable Diseases (NICD) in Johannesburg, gene sequencer Daniel Amoako.
“I didn’t really know how to tell him,” he recalls. She told Amoako, “To me, it seems like a new lineage.”
The discovery of the Omicron variant in southern Africa has caused global alarm, with countries limiting travel from the region and imposing other restrictions for fear that it will spread rapidly even in vaccinated populations.
Amoako and the NICD team spent the weekend of November 20-21 testing the eight samples Viana sent them, all of which had the same mutations, he told Reuters on Tuesday.
It was so strange that Amoako, his colleague Josie Everatt, and other colleagues also thought it must be a mistake. They then recalled that during the week, they had noticed a sharp increase in Covid-19 cases, the kind that could indicate a new mutant.
Additionally, a colleague had alerted Viana to a rarity in the sample earlier this month: an abandonment of the S gene, one of the mutations that now distinguishes the new Omicron variant of the globally dominant delta coronavirus.
The only common variant with that feature was Alpha, “and we hadn’t seen Alpha (in South Africa) since August,” Everatt recalls thinking while testing the samples.
On Tuesday, Nov. 23, after testing another 32 from around Johannesburg and Pretoria, “it was clear,” Amoako said.
“It was terrifying.”
On the same Tuesday, the NICD team informed the Department of Health and other laboratories in South Africa that they were performing the sequencing, which then began to obtain similar results.
On the same day, the NICD entered the data into GISAID’s global scientific database and found that Botswana and Hong Kong had also reported cases with the same genetic sequence.
On November 24, NICD officials and the department notified the 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 abandonment of the S gene, a sign that Omicron was already becoming dominant.
Thanks to Omicron, South Africa’s daily Covid-19 infection rate is expected to quadruple to more than 10,000 by the end of this week, one of the country’s leading infectious disease specialists, Salim Abdool Karim, said on Monday.
The big questions: how good is the new variant at evading immunity from past vaccines or diseases, how severe the symptoms are, compared to previous versions, and how will this differ between age groups, have yet to be answered.
Three scientists interviewed by Reuters who are working on those questions expect answers in about three to four weeks.
Meanwhile, South African President Cyril Ramaphosa is considering introducing mandatory vaccination in some contexts, with the country still recovering from 3 million Covid-19 infections in total during the pandemic and more than 89,000 deaths.
There is much anger in South Africa over foreign travel bans, some of them directed at scientists. Amoako gets some angry messages saying that they should just “stop looking” for new variants.
Wolfgang Preiser, a virologist at Stellenbosch University working on Covid-19, who has also received hate messages, worries that other countries may take this whole saga as a lesson not to be so transparent.
“It could encourage other countries to hide things, or rather, just not look,” he said.
“That is fear. Watching is a great investment, so they might conclude, ‘Let’s not bother.’