South African boffins unpack origins of Omicron that began causing havoc a year ago

South Africa found itself ostracised this time last year for being the “home” of the then newly detected Omicron variant of the virus that causes Covid-19.

Local scientists and the World Health Organisation (WHO), however, said the country had made a breakthrough by discovering a variant that was likely present in several countries already at the time, and was being unfairly labelled as being the origin of the virus itself.

This had caused major restrictions for the country in terms of international travel.

Now, local scientists have made another breakthrough and again, it is to do with the Omicron variant.

A new study led by Stellenbosch University (SU) and published in the journal Science this week shows that predecessors to the Omicron variant existed on the African continent months before cases were first identified.

It also suggests that Omicron emerged gradually over several months in different countries across Africa.

“This important study sheds light on the question of when, where and how the dominating Omicron variant developed,” says Dr Tongai Maponga from SU’s division of medical virology. “The somewhat unexpected results not only enhance our understanding of the novel virus, but provide valuable guidance on how to better respond — and not to respond — to similar situations in the future.”

The study also casts doubt, but does not disprove, two theories on the Omicron variant.

The one is that the virus was transmitted from a human to an animal, where it spread and evolved before infecting a human again.

The other is that it infected a person with a weakened immune system for a prolonged period during which mutations accumulated.

Either scenario could explain how the mutated virus evades pre-existing immunity (after infection or vaccination, or both) and can be transmitted easily between people.

Omicron was the variant with the most mutations and by the end of December 2021, it had replaced the previously dominant Delta variant worldwide.

For the purpose of the study, a PCR (polymerase chain reaction) test was designed to specifically detect the BA.1 lineage of the Omicron variant. It was used to test more than 13,000 respiratory samples from Covid-19 patients collected in 22 African countries between mid-2021 and early 2022.

All samples were tested by researchers within the countries of collection. These tests allowed them to estimate when the Omicron variant started to appear and how fast it spread.

The team concluded that Omicron seems to have evolved in Africa but not necessarily in the two countries in which it was first discovered and shared with the rest of the world. 

This further questions the reasoning behind the travel bans that were placed on South Africa, causing economic losses and other hardships, and which did nothing to prevent the explosive global spread of Omicron. 

Future outbreaks will require better collaboration between countries and measures must not disincentivise global data sharing for the good of humanity, SU said in a statement.

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