Omicron virus “variant of concern”: More transmissible, unknown if otherwise more dangerous

A new “variant of concern” (VOC) for the virus that causes COVID-19 has today been assigned Greek letter “Omicron” by the World Health Organization (WHO) at an emergency meeting of the organization’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE).

In the particular case of the new Omicron variant, designated B.1.1.529 in the PANGOLIN nomenclature, its prevalence where found so far in South Africa and Botswana strongly suggests that it is more highly transmissible than the Delta variant B.1.617.2 it supplanted. “This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant [in patients recovered from infection from another variant], as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa,” the WHO said in a statement.

According to WHO, the first known case of the Omicron variant was found in a specimen collected on Nov 9. According to the PANGOLIN sheet, it was first sequenced for detection on Nov 11.

WHO TAG-VE said that while standard tests are able to detect the Omicron variant, one of its characteristic mutations, called “S gene dropout,” causes one of the components of ordinary polymerase chain reaction (PCR) analysis to fail, and “this test can therefore be used as 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.”

Whether the Omicron VOC exhibits harmful behavior beyond increased transmissibility, such as increased virulence or increased resistance to vaccines and treatments, is not yet known and is unlikely to be known for several weeks, but at this time there is no evidence for it. Vaccines work by training the immune system using proteins present on the outer surface of the virus, so in theory the more mutations a variant exhibits the greater the risk that the immune system trained by either a vaccine or a prior infection will be unable to recognize the variant as effectively.

Promoted from status as a “variant under monitoring” (VUM), the VOC designation of Omicron is the most severe classification, used for variants with significant genetic mutations that demonstrate, at a level of global public health effect, evidence of increased transmissibility, increased virulence, or increased ability to escape tests, vaccines, or treatments. The status of “variant of interest” (“VOI”) is between the two, with evidence of significant mutations and consequence but not yet affecting global public health. WHO assigns Greek letter designations to VOIs and VOCs to aid in public recognition: there are currently four active VOCs (Alpha, Beta, Gamma, Delta) and two VOIs (Lambda, Mu) prior to the new Omicron designation. Variants demoted from VOC or VOI to VUM retain their Greek letters (Eta, Iota, Kappa, Theta).

Shortly after the WHO announcement, President Joe Biden issued a statement that the US would ban travel from a number of African countries: “As a precautionary measure until we have more information, I am ordering additional air travel restrictions from South Africa and seven other countries. These new restrictions will take effect on November 29. As we move forward, we will continue to be guided by what the science and my medical team advises.” Biden further said the best way for Americans to protect themselves is to get a booster shot if they have already been vaccinated and to get vaccinated if not already.

Biden noted the global spread of the pandemic: “Finally, for the world community: the news about this new variant should make clearer than ever why this pandemic will not end until we have global vaccinations. The United States has already donated more vaccines to other countries than every other country combined. It is time for other countries to match America’s speed and generosity.”