Clinical Lab Manager - News, Editorial and Products for the Clinical Laboratory
The new variant harbors 30 mutations in the SARS-CoV-2 spike protein

WHO Names New B.1.1.529 Variant of Concern Detected in South Africa "Omicron"

The new variant harbors 30 mutations in the SARS-CoV-2 spike protein

The WHO has now designated the B.1.1.529 variant recently detected in South Africa as a variant of concern (VOC), naming it Omicron.

According to the WHO, the Omicron (B.1.1.529) variant was first reported from South Africa on November 24, 2021, where the first known case was from a sample collected on November 9, 2021.

First detected via genome-sequencing data from Botswana, the variant is reported to have “concerning” mutations similar to those seen in the Delta and Alpha variants, and compared to other VOCs, there is evidence to suggest the variant has an increased risk of infection.

According to an article published November 25, 2021, in Nature, Omicron has more than 30 mutations in the spike protein—the target our immune system recognizes. These types of changes, also seen in Delta and Alpha variants, have been linked to higher rates of infectivity and the ability to evade our immune system’s antibodies, whether produced as a result of natural infection or immunity from vaccines.  Thus, the worry is that the Omicron variant may be able to evade our immune system, including immunity from vaccines.

At present, the number of cases is so small that it’s hard to know whether this variant will be more transmissible, but it is worrying how quickly it has spread, especially across Botswana, said Richard Van Noorden, features editor, Nature, on the November 26, 2021, episode of Nature's Coronapod podcast.

Many countries have already placed travel restrictions on flights from South Africa.

There are two confirmed cases in Hong Kong from quarantined travelers who were vaccinated with Pfizer vaccines, and reported cases in Israel and Belgium.

Regarding PCR testing, the WHO stated: “Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation.”

According to the WHO, a VOC is “a SARS-CoV-2 variant that meets the definition of a variant of interest (VOI) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

  • increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  • increase in virulence or change in clinical disease presentation; OR
  • decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics.”