Omicron: How was it detected in South Africa & what is known about the high-risk variant?

The World Health Organization (WHO) on Friday classified a new variant with more than 50 mutations first identified in South Africa as a "variant of concern”. Named after the Greek alphabet Omicron strain of the novel SARS-CoV-2  was declared VOC due to "an increased risk of reinfection as compared to other [variants of concern],” WHO announced at a presser, adding that the cases linked with this variant are on the rise in nearly all provinces in South Africa and have spiked over the last 2 weeks prior to its scientific discovery. It is also being noted that the B 1.1.529 Omicron was detected "at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage.”

How was the variant identified in South Africa?

Variant B.1.1.529 dubbed as Omicron by the WHO was first identified in South Africa after it spread among younger people in Gauteng. A routine sequencing conducted by the Network for Genomics Surveillance in South Africa monitored the strange changes in SARS-CoV-2 original genetic makeup, and eventually several South African laboratories observed a new virus lineage, B.1.1.529 of the novel coronavirus in some of the samples. 

Network for Genomics Surveillance in South Africa has served as a valuable tool to better understand the transmission, genetic code, and how the SARS-CoV-2 spreads and is the same system that detected virus lineage, 501Y.V2 named beta variant by the WHO, according to The Conversationist. This genomic surveillance effort was first introduced by the UK in April 2020 and required the genome sequencing of all the samples that tested positive for coronavirus. The process then involves comparing the sequence obtained from different COVID-19 positive diagnosis samples which could detect the changes in the mutations or on the protein spike of the virus that attaches itself to the human ACE receptor. 

When the scientific experts in South Africa noted multiple differences in mutations of the SARS-CoV-2, they alerted the government and further research and investigation went into the genome. Some key contributors in this were South Africa’s well-equipped laboratories such as the central repository of public sector laboratory results at the National Health Laboratory Service, (NGS-SA) the Provincial Health Data Centre of the Western Cape Province, and the country’s modelling expertise. Seventy-seven samples collected in mid-November 2021 in Gauteng province have the Omicron variant. 

It does not seem to be a “daughter of Delta” or “grandson of beta” but represents a new lineage of SARS-CoV-2, with a genetic profile very different from other circulating variants of interest and concern, and allow transmissibility or immune evasion—The Conversationist cited the South African scientists as explaining. 

“South Africa has several laboratories that can grow and study the actual virus and discover how far antibodies, formed in response to vaccination or previous infection,” a report carried by The Conversationist explains. South African scientists were able to determine that the large mutations of this strain, more than 50 and at least 32 on the protein spike made the variant awfully worrisome with respect to its high transmissibility and its high ability to evade COVID antibodies developed from the previous infection and natural or vaccine-induced immunity in fully vaccinated people.

In 2-weeks Omicron transitioned period of 'low transmission' to extremely rapid growth

In a matter of just two weeks, B.1.1.529 variant of coronavirus lineage transitioned from its period of low transmission to extremely rapid growth of new confirmed cases and high circulation across South Africa, the spread this time oddly noted among the youngest people. 

"We're seeing a marked change in the demographic profile of patients with COVID-19," Rudo Mathivha, head of the intensive care unit at Soweto's Baragwanath Hospital, Johannesburg, South Africa told a presser. 

"Young people, in their 20s to just over their late 30s, are coming in with moderate to severe disease, needing intensive care (ICU). About 65% are not vaccinated and most of the rest are only half-vaccinated [with one shot],” said Mathivha.

"I'm worried that as the numbers go up, the public health care facilities will become overwhelmed.” “We need to have critical care ICU beds ready,” she suggested to the countries worldwide. 

Variant B.1.1.529 Omicron may be accounted for as many as 90% of all new cases in South Africa, the health officials mulled, and has a reproduction rate of 2, implying that everyone infected person will transmit it to two others making a chain of infection that is also highly virulent in the community when it spreads. A disturbing number of mutations makes this variant transmissible and evade immune responses. 

"It's a huge, huge concern. We all are terribly concerned about this virus," Professor Willem Hanekom, director of the Africa Health Research Institute, told The Associated Press. "This variant is mostly in Gauteng province, the Johannesburg area of South Africa. But we've got clues from diagnostic tests that suggest that this variant is already all over South Africa," Hanekom, also a co-chair of the South African COVID Variant Research Consortium told the Associated Press agency. South Africa has 40% of all its adult population fully vaccinated,