Inside South African virology labs: Hunting for the next Covid-19 variant

The labs have identified two of the five so-called variants of concern and trained scientists from across the continent on how to gene sequence to spot and track variants

By Janice Kew

As the port city of Durban eases into South Africa’s annual summer holiday season, scientists at a virology laboratory at the Africa Health Research Institute are working around the clock.

The discovery of the Omicron Covid-19 variant by South African and Botswanan scientists last month has lent urgency to efforts to isolate the virus and test its ability to evade vaccines the world is pinning its hopes on to end a two-year pandemic.

The goal is to figure out “what happened? How does it happen? What can we do to decrease it,” said Alex Sigal, 51, who runs the lab that was the first to isolate the beta variant, the Covid-19 strain that’s been most successful in getting past inoculations. We “then figure out a way to quickly adjust our responses,” he said.

Read | Did Covid-19 vaccine inequity allow Omicron to emerge?

South African labs have been critical to combating the coronavirus. They’ve identified two of the five so-called variants of concern and trained scientists from across the continent on how to gene sequence to spot and track variants.

Sigal’s lab was the first to test Omicron against blood plasma from people who’d received two doses of the shot produced by Pfizer Inc. and BioNTech SE. It also updated a paper that hypothesizes that variants may develop in immuno-suppressed people who’re unable to easily shake off the virus, allowing it to mutate.

To many outside medical science circles, the role South Africa-based scientists have played in fighting the pandemic has come as a surprise. But with an HIV epidemic, the world’s biggest, nearing its fourth decade and hundreds of thousands of people infected with tuberculosis, South Africa has been a magnet for the scientists from around the world who track the pathogens that kill us.

The country has set up a network of seven genomic surveillance labs with one at the National Institute for Communicable Diseases and six at academic institutions.

Sigal is Israeli-Canadian and a few floors below his lab in an eight-floor glass and face brick building is Krisp, a gene-sequencing laboratory whose Brazilian head, Tulio de Oliveira, announced Omicron’s discovery to the world.

Read | G7 calls Omicron 'biggest current threat' to world health

“There’s a lot of technical capacity in South Africa to do genomic sequencing of pathogens because we’ve built up that expertise over many years for HIV and TB, ” said Richard Lessells, a Scottish infectious diseases specialist at Krisp. “Very early on in the pandemic, we recognized that genomic sequencing and genomic surveillance was going to be very important.”

Local Talent

With the onset of Omicron that has meant sleepless nights for many of the scientists.

“I’ve been working to get the Pfizer vaccine efficacy study ready,” said Sigal, who becomes animated when he watches a time-lapse video of the Omicron variant attacking cells. “I worked through the night.”

Sigal’s lab has made another important contribution to the country’s ability to monitor changes in the pandemic. When Covid hit, getting supplies across borders became tricky.

The scientists quickly realised they couldn’t get cells in which to culture the virus, so they made their own line from human lung cells that had first been engineered by Sigal while completing his doctorate. This cell line, known as H1299-ACE2, is now being used widely in South Africa in various Covid-19 tests, including Omicron.

Read | Scale-up measures, vax to limit Omicron spread: WHO

Omicron hit South Africa first and so far there’s much to be concerned about. The variant appears to be much more transmissible than earlier variants with daily cases hitting a record this week. Still, hospitalisations and deaths, so far, are substantially lower than in previous waves.

While foreign scientists have flooded into South Africa to tackle the diseases that weigh on a country that straddles the first and third worlds, local talent is robust and developing rapidly.

Sandile Cele, a 33-year-old from a small village near Durban, is part of Sigal’s team of seven scientists who culture cells, spin out plasma and wash test plates. In all, the Africa Health Research Institute, founded in 2016, has 550 students, staff and scientists.

TB, HIV

It was quite challenging to suddenly switch from TB and HIV to coronaviruses, said Cele, who like most of the team is a graduate of the University of KwaZulu-Natal, about two miles from where he works. “But now with the emergence of new variants there is pressure,” Cele said. “For Omicron especially we’re expected to give answers. Everyone has been looking in our direction.”

While Sigal and his team are now focused on Omicron, their aim is to help end the pandemic by getting ahead of a virus that rapidly mutates -- a task that won’t be easy.

We need to start by “understanding how these variants evolve and in doing more surveillance,” he said.

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