In a white coat and mask, Eftyxia Vardas is at the head of an army of laboratory assistants, biochemists and fellow virologists in one of the largest structures of the Lancet private laboratories.

This renowned clinical virologist, who has worked for the last twenty years on the epidemics of tuberculosis and AIDS, is the first to have concluded with her team on the existence of a new variant of Covid-19.

It all started with a few PCR tests ...

At the beginning of November, 22 positive tests, mostly from the capital Pretoria, are the center of all conversations in the laboratory, because what they show is very unusual.

The most widely used PCR tests for detecting cases of coronavirus target three genes.

However, a month ago, scientists realized, to their surprise, that one of the three, the S gene, was no longer detected in the positive results.

Illustrative photo of the Omicron variant of the novel coronavirus, taken in London on December 2, 2021. Justin TALLIS AFP

"We realized that something was different in our PCR tests," Dr. Vardas told AFP, scribbling curves on a notepad.

“We weren't entirely sure what it was, if it was an already existing variant or something new,” she says.

There were four worrying variants at that time: Delta, which so far represented almost all sequenced cases in the world, Alpha, Beta and Gamma.

"Night and day"

The team of scientists then tries not to get carried away.

It takes them about a week to accumulate a sufficient number of samples with the anomaly.

And another week, during which the laboratory runs night and day, to do the sequencing.

Sequencing is a long and expensive process, which allows the genome of the virus present in the body to be deciphered.

"There we got confirmation that something was happening," says Eftyxia Vardas.

"It turned out to be a completely different virus. This is how Omicron was discovered," the scientist said, without any joy.

Omicron variant: John SAEKI AFP peak protein

So convinced that a new variant hitherto unknown is at the origin of the peak of contaminations observed for several weeks in South Africa, she sends the results and the samples to the health authorities.

South Africa is officially the African country most affected by the virus.

The country is experiencing an exponential increase in cases and has more than three million infections, including 90,000 deaths.

The National Institute of Communicable Diseases (NICD), a public biosafety infrastructure and the KRISP, an innovation platform at the forefront of genome research, then set about working on the phenomenon.

They identify that a new form of Covid-19, with an unusual number of mutations and many unknowns, has dethroned Delta.

An employee of a Pretoria morgue in a protective suit takes care of a person who died of Covid, January 22, 2021. MARCO LONGARI AFP / Archives

On November 25, the virologist who became famous for having spotted Beta a year earlier, Tulio de Oliveira, confirmed at a press conference the detection of a new variant in South Africa.

The World Health Organization calls it Omicron.

A new wave of the pandemic, which has killed more than 5.2 million people to date since it emerged two years ago in Wuhan, China, is announced.

In a few hours, the flights were suspended, the world closed its doors to southern Africa.

© 2021 AFP