Why Southern Africa is so good at spotting variants



  • Scientists in South Africa were the first to sound the alarm bells about Omicron, alerting the WHO last Wednesday.
  • But that doesn’t necessarily mean the variant is from southern Africa, rather it’s an indication of the region’s robust surveillance system.
  • “We just rang the bell, which made everyone realize that in fact it may have gone unnoticed,” said a South African virus sleuth.

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Scientists in South Africa alerted the world last week. Omicron is here.

The announcement on Wednesday that virus hunters in this country had found a new variant with dozens of new mutations, alarm bells have sounded in the corridors of the World Health Organization.

Variant B.1.1.529 was first identified on November 11 among the foreign diplomats who have traveled in Botswana. Then it was found by a team of scientists in South Africa on November 14, and they alerted world health leaders. On November 26, WHO designated the newly baptized Omicron a worrying variant.

As researchers around the world rushed to start studying the Omicron – wondering if it spread more easily than Delta; causes more deaths; or requires new vaccines – the US, UK and EU responded to the discovery with swift travel bans, blocking flights from South Africa, Botswana and six neighboring African countries which had not detected the new variant.

It is thanks to Southern Africa that the rest of the world is on high alert, rushing to answer these important public health questions.

The reality is that Southern Africa is one of the major international powers in COVID-19 monitoring in large part because the continent has innovative systems in place to track viral diseases and genetic mutations long before the coronavirus struck, tracking and monitoring diseases such as HIV, Ebola and tuberculosis.

“We had a very good research experience with our universities, as well as with the different research consortia,” said Vicky Baillie, senior scientist at the Wits Vaccines & Infectious Diseases Analytics research unit in South Africa.

“A lot of it was put in place and we had a lot of experience – so I think we were in a very good position to respond to COVID. “

Chances are, Omicron came from elsewhere in southern Africa.

It’s unclear (and largely irrelevant at this point, given the extent of the variant’s circulation at this point) exactly where the new variant emerged.

It is suspected that generic variants like Omicron, with several dozen new changes in the genetic sequence of the virus, often originate from a single immunocompromised host, which cannot put up appropriate defenses against the virus, and therefore incubates the virus. as it replicates. for months and months.

“Given the alphabet soup of mutations, I think it’s probably more likely that this is the result of ongoing molecular evolution within a single host that has spread to the population, ”said Charity Dean, CEO and co-founder of The Public Health Company, of the theory that this new variant came from a single immunocompromised person.

“But I think it’s unfair to blame South Africa when it may very well come from another country or another continent. And in the end, it doesn’t matter. They deserve incredible recognition for spotting it, making it public, transparently sharing everything they know, ”Dean said.

Despite praise from scientists and public health professionals like Dean, the resentment of the general public has hurt African scientists who have worked tirelessly to educate the world about these emerging variants, before it is too late.

‘It was really tough,’ Baillie, the South African virus watcher who often shares glimpses of her coronavirus sample sequencing work on TikTok, noted. “There has been a lot of backlash against the scientific community in South Africa with a lot of people saying, ‘Well, thank you very much for identifying this. It means we don’t have a Christmas vacation. “”

Why Southern Africa detects variants faster than the United States

For decades, Africa has focused on developing and setting up futuristic disease monitoring surveillance systems, often in partnership with funders public and private in the US and UK. The United States National Institutes of Health, the United Kingdom’s Wellcome Trust health research foundation, the Centers for Disease Control and Prevention, the Bill and Melinda Gates Foundation and others have all contributed significant amounts of money and time to the rise of viral surveillance systems in Africa.

there is the Human Heredity and Health in Africa Initiative (H3Africa), who discovered millions of unique genetic variants, applause from NIH Director Francis Collins. And then there’s the Botswana Harvard Partnership, another collaboration established in 1996 to fight the HIV epidemic. This is where the Omicron variant was first spotted earlier this month, per Sikhulile Moyo’s laboratory.

During the first months of the pandemic, South Africa also drew up a new South Africa Genomic Surveillance Network (NGS-SA). Although the network technically sequences fewer coronavirus samples than in the United States done on a per capita basis, it does so more strategically, sampling randomly across the country.

“We just rang the bell, which made everyone realize that in fact, maybe it was going unnoticed,” Baillie said of the Omicron detection.

Since this alarm was triggered, Omicron has already been detected in Canada, Germany and at least 16 other countries around the world except Botswana and South Africa. Scientists from The Netherlands discovered in recent hours that the Omicron variant was already in this country for at least a week.

Travel bans may discourage science

smiling scientist inside his genome sequencing lab

Vicky Baillie performs the type of genomic sequencing that detects new variants of the coronavirus.

Courtesy of Vicky Baillie


Health experts say South Africa’s experience last week could discourage other countries from being quick and transparent about what the virus is doing inside their borders, knowing that such honesty could turn out to be punitive.

Letting the world know that Omicron is on the move dealt a quick and shocking blow to the economy of southern Africa. South Africa the rand and the stock market are just starting to recover of the stigma that Omicron has unleashed on the national economy, and international travel during the southern hemisphere’s summer vacation season is largely frozen.

The United States has recognized the role of southern Africa. Today, Dr Anthony Fauci, America’s foremost infectious disease expert, congratulated South Africa in a White House COVID-19 Briefing. His applause echoed President Biden, who said on Monday that South Africa should get “credit” for “promptly briefing the world” about Omicron. But that was the same day his travel ban in southern African countries went into effect.

“We really need to figure out what our goal is with these travel bans,” said Dr. Nahid Bhadelia, infectious disease expert and director of the Center for Emerging Infectious Diseases Policy & Research at Boston University. Dr Kevin Pho in his Sunday podcast.

“Are you setting an example that really decreases the willingness of countries to share future data?” “

After all, US citizens can always come back to the United States from southern Africa, provided they are vaccinated and test negative for the virus.

“We ask ourselves: why can’t we do this for everyone? »Said Bhadélia. “We should do it anyway, for anyone coming from anywhere else, if we really want to use the slowdown through travel restrictions.”


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