How South African Scientists Discovered the Omicron Variant

Tit starts with unusual PCR tests. One afternoon on November 4, a scientist, Alicia Vermeulen, spotted an anomaly in a test result. A positive test, but did not detect the S gene, the one that produces the Spike protein and which is one of the three genes that are usually used to confirm the positivity of a test. This is called a deletion, and it is a clue that the gene may have been mutated. “It immediately aroused my curiosity,” she told the news site News24. “We wanted to know what caused this deletion of the S gene, because it looked like what we had previously observed with the Alpha variant. “

As the number of tests exhibiting this characteristic increases over the days, Lancet scientists decide to sequence a sample in Johannesburg. “We assumed it was a variant, but we didn’t know which one,” says Professor Eftyxia Vardas, a virologist at Lancet Laboratories. “It was when it was sequenced that the scientists responsible for it realized that it was a completely new variant. The sequenced genomes are then sent for analysis to the National Center for Infectious Diseases.

“It was impossible that there were so many mutations! “

It is 9 p.m. on Friday, November 19, when at the National Center for Infectious Diseases, researcher Jinal Bhiman and her team receive the first analytical results of these strange PCR tests. As the genome appears on the computer screen, Jinal and his colleagues can’t believe their eyes. “Our first reaction between the four of us was: No, there is a problem, it is a mistake. It was impossible that there were so many mutations in a single sequence. We couldn’t believe our results! “

The sequence has 50 mutations, four to five times more than for the previous variants. The Spike protein alone has 32. Jinal Bhiman and his team then decide to redo the analysis. Twice, that weekend, they started again, but each time obtained the same result. “We therefore decided to carry out the analysis through a different channel, to be really sure, and on Monday we had confirmation that this was true. “

The National Center for Infectious Diseases then announced the discovery to the government, then to the WHO, and between Tuesday and Thursday all the diagnostic centers multiply the analyzes of PCR tests by focusing on this S gene. Thursday, November 25, the KRISP, The KwaZulu-Natal Research, Innovation and Sequencing Platform announces the discovery of a new variant at a government press conference.

A controversial early announcement

In fact, the first sequencing of the B1.1.529 variant, later dubbed Omicron, was not performed in South Africa, but in Botswana on November 11, then in Hong Kong on November 13.

When South Africa first announces the existence of Omicron, it is keen to assert itself as a transparent player in the fight against the epidemic. A transparency that will be rewarded in words, but hardly in deeds: in a few days, dozens of countries close their borders to South Africa, the same who declare – like the American Minister of Foreign Affairs – that “the South Africa’s transparency should set an example to the world ”. These hasty reactions are seen as a sanction by residents and researchers.

“I was extremely disappointed by this response from the rich countries”, regrets Jinal Bhiman. “Instead of trying to fix the problem, they made it worse. Many people have lost their jobs in South Africa, and tourism is an important part of our economy. Canceling the flights had a terrible impact, economically, but also on the morale of the entire population. “All the more so since the variant is already present in many countries, for example sequenced from November 19 in Germany.

But in South Africa, you don’t just blame foreign countries. Many criticize scientists for revealing the existence of the variant too early. At Lancet Laboratories, Eftyxia Vardas believes it would have been appropriate to wait to learn more before panicking the world. “I think it’s important to fully understand the impact of a variant before making a big public announcement. It hurt the country a lot. “

The authorities explain the desire to have wanted to warn health professionals as soon as possible, so that they can anticipate and perhaps adapt their holidays, while the summer holidays are just starting in the country. “We have sounded the alarm because infections are increasing rapidly,” defends Professor Tulio de Oliveira, a researcher at KRISP who made the variant public on Twitter. “We did this to protect our country and the world despite the possibility of massive discrimination. “

One thing is certain, the consequences of South African transparency set a sad precedent for research. Not sure that the scientists who discover the next variant will risk revealing it so soon.