‘Stealth’ Omicron Variant Is Difficult for Researchers to Identify, Track

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Researchers in South Africa say the omicron variant known as BA.2 has become the dominant strain of COVID-19 in the country weeks after it was identified.

The strain accounts for nearly 100% of new infections, prompting one of the nation’s leading COVID-19 researchers, Professor Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation at Stellenbosch University, to ask on Twitter: “What does it mean?”

Researchers and public health experts across Africa are asking the same question as the BA.2 subvariant proves itself to be 1.5 times more transmissible than its parent variant, which was itself up to 40% more transmissible than the delta variant that preceded it.

Since it was detected, the BA.2 subvariant has turned up in Botswana, Kenya, Malawi, Mauritius, Mozambique and Senegal, according to the Africa Centres for Disease Control and Prevention (Africa CDC).

“If a country hasn’t reported it, it’s not because it’s not there. It’s because their surveillance systems are not strong enough,” Africa CDC Director Dr. John Nkengasong said during a recent press briefing.

Omicron infections are milder than previous variants and carry a lower risk of hospitalization, but they still can be deadly. The World Health Organization (WHO) estimates that 500,000 people around the world have died from COVID-19 since the omicron variant arose.

At this point, it appears that a BA.2 infection creates immunity to other versions of omicron, according to Professor Francois Balloux, director of the University College London’s Genetics Institute.

De Oliveira posted a chart showing the BA.2 subvariant rapidly growing over the past few weeks from less than 25% of omicron cases as the fourth COVID-19 wave peaked in South Africa around the end of 2021.

De Oliveira pointed out that new cases of COVID-19 in South Africa have declined sharply from their peak at the end of 2021. However, the small number of cases being detected are all BA.2.

De Oliveira said reduced community testing and BA.2 clusters in schools have made the current understanding of the subvariant “quite messy.”

“We need to be careful on the interpretation of increase of BA.2 and clustered outbreaks,” he said on Twitter.

Scientists have identified four subvariants of the omicron strain of COVID-19. The BA.2 subvariant has raised concern because it does not contain a key component that researchers use to identify it through genetic-based PCR tests and track its spread. The fact that BA.2 is difficult to identify has prompted some to call it the “stealth variant.”

It’s unclear where BA.2 emerged first, but it was found in genetic material submitted to the global COVID-19 database by researchers in the Philippines.

Variants and subvariants are a natural part of the COVID-19 virus’s evolution. The more it spreads through the population, the more chances it gets to create new variants that can spread quickly or evade the human immune system. The delta variant, which sparked Africa’s third wave of infections in mid-2021, created 200 subvariants.

So far, the BA.2 subvariant has shown no signs of causing breakthrough infections  the way previous variants have done.

The appearance of a stealth variant is a reminder that the pandemic hasn’t ended and that COVID-19 remains a potential threat worldwide, experts say.

“We’re watching this virus evolve in real time,” WHO epidemiologist Maria van Kerkhove said during a recent briefing.