Omicron SARS-CoV-2 variant: Unique features and their impact on pre-existing antibodies

J Autoimmun. 2022 Jan:126:102779. doi: 10.1016/j.jaut.2021.102779. Epub 2021 Dec 13.


Severe Acute Respiratory Coronavirus (SARS-CoV-2) has been emerging in the form of different variants since its first emergence in early December 2019. A new Variant of Concern (VOC) named the Omicron variant (B.1.1.529) was reported recently. This variant has a large number of mutations in the S protein. To date, there exists a limited information on the Omicron variant. Here we present the analyses of mutation distribution, the evolutionary relationship of Omicron with previous variants, and probable structural impact of mutations on antibody binding. Our analyses show the presence of 46 high prevalence mutations specific to Omicron. Twenty-three of these are localized within the spike (S) protein and the rest localized to the other 3 structural proteins of the virus, the envelope (E), membrane (M), and nucleocapsid (N). Phylogenetic analysis showed that the Omicron is closely related to the Gamma (P.1) variant. The structural analyses showed that several mutations are localized to the region of the S protein that is the major target of antibodies, suggesting that the mutations in the Omicron variant may affect the binding affinities of antibodies to the S protein.

Keywords: B.1.1.529; COVID-19; Omicron variant; SARS-CoV-2; Variants.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Antibodies, Viral / immunology*
  • Binding Sites
  • COVID-19 / immunology
  • COVID-19 / virology*
  • Humans
  • Mutation
  • Phylogeny
  • Protein Structure, Tertiary
  • SARS-CoV-2 / genetics*
  • Spike Glycoprotein, Coronavirus / genetics


  • Antibodies, Viral
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Supplementary concepts

  • SARS-CoV-2 variants