Omicron Variant of SARS-CoV-2

Aditi Bhargava
5 min readDec 2, 2021

Omicron variant of SARS-CoV-2 by all original accounts, is milder. According to Dr. Angelique Coetzee, Chair of South African Medical Association, “very mild” symptoms that differed from the dominant Delta variant were noticed in seven patients at her clinic. An alert technician noticed a different RT-PCR pattern and sequencing revealed a new, hitherto unreported variant. The Omicron (B.1.1.529) variant has specific deletions that is also shared by the Alpha and Eta variants. It has insertion mutations (addition of 3 amino acid residues) along with a cluster of mutations in the S1-S2 furin site. In addition to mutations in the spike protein region, it also has mutations in the nucleocapsid region of the virus. Phylogenetic tracing suggests that Omicron variant is more closely related strains circulating in the early-to-mid-2020 than more recent ones. This variant is also reported in Botswana and Hong Kong. And today, December 1, 2021, the first patient with Omicron variant was identified in San Francisco, USA. This patient was fully vaccinated and like South African patients, also has mild symptoms.

The website covariants.org describes in detail all SARS-CoV-2 variants and mutations.

If Omicron variant is even more transmissible than the Delta variant, but so far, much milder symptoms in both unvaccinated and vaccinated, then it strongly suggests, the virus is trying to mutate to a less virulent or pathogenic variant so that it can become endemic. Also, if the unvaccinated people do not have severe symptoms or need hospitalization and their symptoms are comparable to those fully vaccinated, it is unclear how it can be concluded that vaccines are effective in preventing transmission and reducing symptoms.

Before the calls to get booster become deafening, it would be prudent to get some answers.

1. If this variant has infected both the vaccinated and the unvaccinated, do the symptoms differ between the two groups? It appears that so far, no one infected with this variant has been hospitalized and all have mild symptoms, irrespective of vaccination status.

2. It seems very unlikely that Omicron variant originated independently in 3 different countries simultaneously. Given the stringent tracking and contact tracing efforts, it should be possible to narrow down the location of its origin.

3. Has anyone who has recovered naturally from COVID, but remains unvaccinated, has gotten re-infected with Omicron.

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Aditi Bhargava

Dr. Aditi Bhargava is a molecular neuroendocrinologist with research focus on sex differences in stress biology and immunology.