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Angle: South African researcher shocks when discovering Omicron strains | Reuters

[Johannesburg, 30th Reuters]-It was November 19th. Raquel Baiana, head of science at South Africa’s largest private laboratory, Lancet Laboratory, was shaken by a genomic sequence analysis of eight samples of the new coronavirus.

It was November 19th. Raquel Baiana, head of science at South Africa’s largest private laboratory, Lancet Laboratory, was shaken by a genomic sequence analysis of eight samples of the new coronavirus. The photo is a nurse preparing a vaccine in Eastern Cape. Taken on the 29th (2021 Reuters / Siphiwe Sibeko)

This is because all the samples showed many mutations. Most notable are mutations in the “spiked protein” that the virus uses to invade human cells.

“I was terribly shocked by the sight. I wondered if I had done something wrong,” Biana told Reuters. However, the idea soon changed to “a painful feeling that this sample causes a very big problem.”

She immediately called her colleague Daniel Amoako, a genomic analysis expert at the National Institute of Infectious Diseases (NICD).

“I didn’t know how to cut it out,” he said. “It looks like a new stock to me.”

The discovery of a new mutant of the new coronavirus, the Omicron strain, in South Africa has sounded alarms around the world. Fearing that the infection could spread rapidly among vaccinated people, countries have taken restrictions on travel from the region and other restrictions.

NICD’s Amoako and his team inspected eight samples sent by Biana on the weekend of November 20th and 21st. Amoako told Reuters that the same mutation was found in all samples.

Oddly enough, Amoako and his colleagues also thought it must be something wrong. I remembered the number of new coronavirus infections that had surged over the weekend, as if they were showing the emergence of new mutants.

Biana also noticed that a sample recently tested by a colleague had a mutation called the “S gene dropout.” This mutation is currently one of the distinguishing features between Delta and Omicron strains.

Of the other common mutant strains, only the alpha strain has this characteristic. “And I haven’t seen Alpha stocks since August (in South Africa),” recalls Josie Everat, a member of Amoako’s team.

By November 23, 32 additional samples from Johannesburg and the Pretoria area had been inspected “no doubt,” Amoako said.

“It was scary.”

On the same 23rd, the NICD team reported the results to laboratories throughout the country conducting genome analysis, and similar results began to appear at these institutions.

On the same day, NICD entered the test results into the database of GISAID, an international virus information sharing organization, and learned that cases of the same gene sequence were reported in Botswana and Hong Kong.

The following day, 24th, NICD executives and departments reported to the World Health Organization (WHO).

By this time, more than two-thirds of positive testers had S gene dropouts in Gauteng, which includes Pretoria and Johannesburg, Biana said. It’s a sign that the Omicron strain has already become the dominant strain.

South Africa’s leading infectious disease expert, Salim Abdul Karim, said on November 29 that the number of new infections in South Africa will quadruple to more than 10,000 by the weekend due to the Omicron strain. ..

The remaining important questions are 1) whether the Omicron strain can bypass the immune function of vaccines and past infections, 2) how severe it is compared to existing strains, and 3) whether the severity varies depending on the age group. ── and so on.

Three scientists interviewed by Reuters expect these questions to be resolved within three to four weeks.

On the other hand, in South Africa, there is a great deal of anger at the travel bans of other countries, and some of them are also directed to scientists. Amoako received several angry messages that she should have stopped investigating new stocks.

Wolfgang Pleaser, a virologist at Stellenbosch University working on the new corona research, also received a hatred email. He is concerned that foreign countries may be reluctant to disclose information based on the lessons learned from this end.

“It may motivate other countries to hide the facts or even refrain from testing. I’m afraid. Inspection requires a considerable investment, so’Let’s stop testing. “Maybe,” Mr. Pleaser thought.

(Tim Cocks reporter)

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