Laboratories in South Africa’s Gauteng province in early November started to witness something strange when they were processing Covid-19 tests. The scientists could not detect the virus gene in the test samples that create the spike protein allowing the pathogens to invade the human cells and later spread. 
During the same time, doctors in the region were witnessing a sudden rise in patients who complained of fatigue and headaches. These fresh cases emerged after weeks of silence that occurred following a delta variant that caused the third wave of Coronavirus in the country that unleashed chaos through Johannesburg and the capital Pretoria in July.
The latest developments have facilitated the beginning of a wave of infections which has been named the Omicron variant, which quickly became a powerful strain and prompted a new surge in Covid cases. 
The discovery of the Omicron variant was announced on November 25 has triggered a global panic and market collapse. Several countries including the UK, US have implemented bans on flights to and from South Africa, while by Tuesday the Omicron mutant has been identified in at least 15 countries. 

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The scientists at a privately-owned Lancet Laboratories had first discovered the abnormalities in the samples, who had raised the red flag, said 
"They didn't know what was wrong so they alerted the virologists, who began to sequence the samples," she said in an interview taken on November 29. 
Junior Lancet scientist Alicia Vermeulen was attributed with the preliminary findings on the afternoon of 4 November after she noticed a peculiarity in a single test that came positive and later informed her manager, as per News24, a South African news website. 
In the next week, similar abnormalities were seen in several cases and Allison Glass, head of molecular pathology at Lancet and a member of the government's Ministerial Advisory Council on Covid-19, was told, the website stated. 
The National Institute for Communicable Diseases and the Lancet together by November 22 were able to discern that there was a new strain which was initially known as B.1.1.529, reported News24. 
The report said that the S-gene couldn't be identified because it had mutated. 
Meanwhile, scientists in Botswana had also found the same anomalies in samples from tests that were conducted on travellers in early November and reports also said that in a sample taken from a person who had returned from Hong Kong from South Africa and was in quarantine, had shown the presence of Omicron variant. 
The data was uploaded onto GISAID, a global repository was leaked in a flash and by 24 November the British media had presented the initial reports about the new strain of Covid-19. 
On November 24, Nicholas Crisp, the acting director-general of South Africa’s Department of Health confirmed that he was briefed in the evening and other government officials of importance were informed the next day. An urgent press conference was convened where Tulio de Oliveria, the head of two gene-sequencing institutes in South Africa, announced the discovery.

Also Read: Omicron variant can be detected by RT-PCR, RAT: ICMR chief

As the omicron strain’s initial outbreak occurred in a relatively young cohort of college students, the severity of the disease is mild. Doctors are of the opinion that the effects of the disease in older and more vulnerable parts of the population will be unpredictable. 
Gray said, "Whatever I tell you today may be false tomorrow.
The mutations of the omicron has led the World Health Organisation to warn of “severe consequences” from covid surges as the strain is capable of being more transmissible and evading the immunity from vaccination and earlier infection.
South Africa’s gene-sequencing capabilities are the reason behind the nation’s rapid discovery. These capabilities were built with the help of research funding that was provided to tackle other diseases like HIV, which is more prevalent in the country and the tuberculosis epidemics, which are the largest in the world.

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