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A new variant of the COVID virus has been discovered. It was labelled as the Omicron Variant or B.1.1.529. It is hypothesized that the origin of this variant is not in South Africa. This article will shed some light on why South Africa was initially perceived as the country of origin for this new strain.

Why the misconception on the Origin?

Since the outbreak of HIV, the Global community has poured billions of funds into South Africa for researchers and scientists to do research on the HIV virus to find a cure or some form of remedy. This resulted in South Africa to grow some of the world’s leading scientists in the field of virology. Having said that, South African scientists were constantly testing and researching a multitude of different viruses on an ongoing basis. The COVID virus was among the research subjects. The misperception of the origin of the COVID virus and the link to the origin in South Africa is understandable, however, because of HIV research and because South Africa developed some of the leading scientists in the field of virology, our scientists were the first to recognize this new variant. When they confirmed the new variant through multiple testing and re-testing,  the NICD entered the data into the GISAID global science database.The NICD officials and the Department of Health notified the World Health Organization.

Because this database is shared among countries, societies immediately jumped to the conclusion that the virus originated from South Africa. The fact is, it didn’t originate from South Africa. It was FOUND by South African scientists thanks to their rich history in research since the HIV era.

How South African scientists came across the Omicron variant

According to IOL ,On Friday, November 19, Raquel Viana, the Head of Science at Lancet laboratories, a leading brand in South African Pathology, sequenced the genes on eight coronavirus samples – and got the shock of her life.

The samples, tested in the laboratory, all bore a large number of mutations, especially on the spike protein that the virus uses to enter human cells.

“I was quite shocked at what I was seeing. I questioned whether something had gone wrong in the process,” she told Reuters, a thought that quickly gave way to “a sinking feeling that the samples were going to have huge ramifications”.

She contacted her colleague at the National Institute for Communicable Diseases (NICD) in Johannesburg, South Africa, a gene sequencer named Daniel Amoako.

“I didn’t quite know how to break it to them,” she recalls. She told Amoako, “To me, it looks like a new lineage.” IOL reports that The discovery of the Omicron variant in Southern Africa has caused global alarm, with countries limiting travel from the region and imposing other restrictions for fear it could spread quickly even in vaccinated populations.

Amoako and the team at the NICD spent the weekend of November 20-21 testing the eight samples which Viana had sent them, all of which had the same mutations, he told Reuters.

It was so bizarre that Amoako, his colleague Josie Everatt and other colleagues also thought it must be a mistake. Then they remembered that over the week they’d noticed a sharp rise in Covid-19 cases, of the sort that might indicate a new mutant.

The missing “S”

According to the World Health Organization, this variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected. The gene is called the “S-gene”. The  dropout or S gene target failure test can be used as a marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.

Why the virus is called Omicron

Omicron is a Greek number (Greek alphabet — Alpha, Beta, Gamma, Delta etc.). There are different variants of COVID and this one is the 15th one. The WHO uses the Greek counting terminology to number and name the different variants of COVID. The name Omicron variant is the most common way to refer to the COVID-19 variant that’s technically known as B.1.1.529.

In Conclusion

In many countries, scientists test and monitor thousands of viruses and bacteria each day in an attempt to prevent a pandemic or to develop vaccines as a precaution or contingency. Global society prematurely labelled South Africa as the origin of the virus. SA scientist merely tested the mutated CoronaVirus and found a dependency in a missing S-gene. They identified and reported the finding to a global WHO database where other countries may view the findings. Instead of accusing SA as the originator of this variant, we should rather commend SA scientists for detecting this new variant at a time where a pandemic can be prevented through early detection.

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