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Omicron BA.2 Harder to Identify, Reportedly in 5 African Countries

Expertly reviewed by Dexter Macalintal, MD · Internal or General Medicine

Written by Jason Inocencio · Updated Mar 09, 2022

Omicron BA.2 Harder to Identify, Reportedly in 5 African Countries

Five African countries have registered the BA.2 sub-variant of Omicron. A World Health Organization (WHO) scientist expressed concern that BA.2 samples may not be spotted as a form of Omicron. The Omicron strain of COVID-19  currently making its way worldwide is designated BA.1. Omicron BA.2 has begun to replace BA.1 in Denmark and another WHO official notes no difference in disease severity between the two. The five African countries identified with BA.2 are Botswana, Kenya, Malawi, Senegal, and South Africa.

Omicron BA.2 harder to identify

The World Health Organization’s Dr. Nicksy Gumede-Moeletsi shared the information in an online media briefing on February 3. She added that BA.2 was proving hard to identify because it was not always picked up by the S-Gene Target Failure criterion. The original Omicron is distinguished from other variants using this criterion.

Gumede-Moeletsi said the WHO was working very closely with laboratories. The organization is asking laboratories to forward samples that had come back without being flagged as Omicron for further analysis. The purpose of the analysis is to gain a more precise picture of the spread of BA.2.

The WHO does not yet consider BA.2 to be a distinct “variant of concern.” The agency is continuing to monitor how it spreads.

Monitoring BA.2 like Delta

The Omicron BA.1 variant or the “original” Omicron is supposedly easier to track than others. BA.1 is missing three target genes found in a common PCR test. Cases showing this pattern were assumed to be caused by BA.1 by default.

The BA.2 that is sometimes identified as a “stealth” sub-variant is a different case. BA.2 does not have the same missing target gene as the original Omicron BA.1 does. “BA.2 shares over 30 mutations with BA.1, but it also has 28 unique mutations,” says evolutionary geneticist and advisor to the Central Virology Laboratory in Israel Shay Fleishon.

Some countries are reporting that BA.2 is taking over the original Omicron strain in terms of dominance. It is now the dominant strain in Denmark and in parts of India and the Philippines. Denmark was the first European Union country to lift COVID restrictions just last week. Denmark also reported more than 50,000 new infections in just one day two weeks ago.

BA.2 origins

A bioinformatician at the Biozentrum of the University of Basel in Switzerland shared some insights on the origins of BA.2. Cornelius Romer says the BA.2 variant likely arose from a common ancestor around the same time as the original BA.1 Omicron. He therefore considers the newer variant a “sibling” rather than a “descendant.”

An evolutionary virologist at the Fred Hutchinson Cancer Research Center and a Howard Hughes Medical Institute investigator had another take. Jesse Bloom hypothesizes that BA.1 dominated first simply because it started spreading earlier. He notes that BA.2 is now catching up.

Early estimates by Denmark’s State Serum Institute suggest Omicron BA.2 is about 50% more transmissible than the BA.1 strain. The United Kingdom Health Security Agency suggests that BA.2 is more transmissible but only 30% higher than BA.1. Experts are however saying that BA.2 will not likely cause a spike in severe infections.

The UK Health Security Agency also estimates that existing vaccines are equally effective at preventing symptomatic diseases caused by both BA.2 and BA.1. Their data is based on a relatively small number of cases though.

Key Takeaways

The World Health Organization expressed concern that the Omicron BA.2 sub-variant is now in five African countries. Botswana, Kenya, Malawi, Senegal, and South Africa have registered the sub-variant. Omicron BA.2 is already overtaking the original BA.1 Omicron as the dominant strain in Denmark. Both strains likely came from a common strand although BA.1 just started spreading earlier. Current vaccines in the market are equally effective in combatting both strains of the coronavirus.

For more on Coronavirus, click here.


Hello Health Group does not provide medical advice, diagnosis or treatment.

Expertly reviewed by

Dexter Macalintal, MD

Internal or General Medicine

Written by Jason Inocencio · Updated Mar 09, 2022

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