Highly Mutated Omicron Variant Becomes Dominant Strain in South Africa

ADF STAFF

The highly transmissible, highly mutated BA.2 subvariant of COVID-19’s omicron strain has become the dominant strain in South Africa and is spreading quickly.

“It really is quite incredible how quickly omicron has overtaken delta [variant] around the world,” Dr. Maria Van Kerkhove, an epidemiologist with the World Health Organization (WHO), said during a recent briefing on the status of COVID-19.

Since omicron first appeared in November 2021, researchers have detected four subvariants, with the BA.2 strain showing the greatest ability to spread and outpace the original strain, BA.1.

As of mid-February, 75% of African countries had reported at least one case of omicron. The Africa Centres for Disease Control and Prevention tracks the main variants but does not report subvariants. In nine countries, omicron has created a fifth wave of infections.

“If a country hasn’t reported it [omicron], it’s not because it’s not there,” Africa CDC Director Dr. John Nkengasong said recently. “It’s because their surveillance system’s not strong enough.”

South Africa’s omicron cases peaked December 18, about one month after it was first reported. The decline started out equally quickly but didn’t fall to the low levels officials had hoped for.

Van Kerkhove said the WHO is concerned that BA.2 may cause a new rise in omicron cases in countries such as South Africa, where the BA.1 strain has peaked or passed.

“We’re looking not only at how quickly those peaks go up, but also how quickly they go down,” Van Kerkhove said. A slow decline could mean the BA.2 subvariant is spreading.

Tracking BA.2 and other omicron subvariants has become difficult in part because COVID-19 testing has begun to decline.

“We can’t fight this virus if we don’t know what it’s doing,” WHO Director-General Dr. Tedros Adhanom Ghebreyesus said during a recent briefing.

Blood tests suggest that omicron is more widespread than testing reveals, according to the WHO.

Nkengasong reported that testing in Africa is down 14% from previous highs. Elsewhere, testing has declined even more.

Deaths from COVID-19 — including omicron and delta variants — are on the rise. In mid-February, 75,000 people died from COVID-19 worldwide. At the pandemic’s peak, 110,000 people died in a single week.

“We’re seeing the number of cases appearing to fall away and yet the number of deaths is increasing,” said Dr. Mike Ryan, the WHO’s executive director for health emergencies.

With countries reopening, citizens feel less pressure to get tested, Ryan said.

As a reflection of that new reality, South Africa recently announced an end to nationwide restrictions in favor of a localized approach that can target outbreaks.

Ryan said that what works for one country may not work for another. Every country needs to chart its own path out of the pandemic, he said.

“Not all paths are straight,” he said.

In South Africa, according to at least one study, 80% of the population has been exposed to COVID-19, providing widespread immunity to infection. Other countries have much lower numbers of exposure or immunity.

“Right now, we’re in a period of great uncertainty,” Ryan said. “The urge to open up is so high that we may overshoot the runway.”