On Thursday, November 2021, South African health officials announced that they had identified a new variant of the pandemic virus SARS-CoV-2, which causes COVID-19; the variant now has a lineage designation of B.1.1.529. (Update: The World Health Organization has now designated it a Variant of Concern, and named it "Omicron, in line with naming protocols.") Its genome is packed with mutations (compared to the SARS-CoV-2 virus that emerged in December 2019). The variant has now been identified in travelers to Belgium, Hong Kong and Israel, and in southern Africa. Intial reports have suggested that the Omicron variant causes mild illness, even in the unvaccinated; that may change.
Health officials said that this new variant is causing COVID-19 infections to surge again, though right now, fewer than 100 genomes of the variant had been collected from patients - there is still a lot to learn. On Wednesday of this week, the number of infections recorded that day spiked at around 1,200; the daily infection rate had been about 100 earlier this month.
South Africa's Health Minister Joe Phaahla noted that this exponential increase in cases indicated that the variant warrants "serious concern" and has the potential to become "a major threat."
However, Dr. Maria Van Kerkhove, the COVID-19 Technical Lead at the World Health Organization noted that we don't yet know very much about this virus. She stressed that the variant was quickly detected, so the surveillance systems that are in place seem to be working. Researchers are now beginning to investigate the variant, and what impact it may have on diagnostic tests, treatments, and vaccines.
There are many mutations in the new B.1.1.529 variant, more than the Delta or Beta variants. The mutations seem to result in 30 changes to the viral spike protein. The number of mutations may not matter, though, the focus is on what those variants do to the virus. Right now, we don't know if they make the virus more infectious, or whether they cause more serious cases of illness. But experts are concerned; many of these new cases are appearing in young people.
The upcoming holiday season also has many health officials in different countries predicting a new wave of infections, including in South Africa, even though it's summertime right now in the Southern Hemisphere. A fourth wave had been anticipated to arrive around the middle of December, but that was before the emergence of the new variant was confirmed.
So far, genetic sequencing has identified 77 cases of COVID-19 caused by the B.1.1.529 variant, according to the National Institute for Communicable Diseases (NICD). Many more samples are undergoing analysis or will be soon. A cluster outbreak also occurred that was centered at a higher education institute in Pretoria. Case numbers are rising quickly in some areas of South Africa.
Only 35 percent of the South African population is fully vaccinated, highlighting the need for countries with better access to vaccines to quickly and equitably share their vaccines and their knowledge with the entire world. A major, global vaccination campaign would benefit everyone.
Sources: Nature, Medical Xpress, WHO