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The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanisms

Willett B.J. et al. (MedRxiv) DOI: 10.1101/2022.01.03.21268111

The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanisms


  • SARS-CoV-2

  • Omicron

  • Endosomal Entry

Main Findings

SARS-CoV-2 Omicron has rapidly become the dominant variant worldwide. Early sequencing of the Omicron variant in South Africa alerted investigators to the possibility that Omicron was a variant of concern because of extensive mutations in the spike protein. Omicron has 30 mutations in the spike protein compared to the original Wuhan-Hu-1 variant, with 15 mutations in the receptor binding domain linked to decreased antibody binding, mutations in the s1/s2 furin site found to enhance furin cleavage and increase infectivity, and mutations in the amino terminal domain that is the primary binding site for a few therapeutic antibodies used to fight COVID-19 infections (Willett et al.). Many new studies are detailing the increased infectivity of Omicron owing to these mutations, however, how these mutations affect viral entry and lung cell infectivity is not well understood.

Willet et al. sought to functionally define Omicron and how it compares to previous strains. The authors’ first findings were that in Calu-3 (lung epithelial) cells there was a significant reduction in Omicron viral copy numbers over time compared to the Delta variant and Wuhan-Hu-1.These findings hint at a mechanism that could contribute to reduced disease severity seen in SARS-CoV-2 Omicron infections.

The authors also found that Omicron infection does not trigger the formation of syncytia between cells, which has been associated with the increased disease caused by previous variants of concern. To examine syncytia formation, Willett et al. used the split GFP system where the complete protein GFP is only formed by cells that were fused together and they noted a reduction in GFP levels over time with Omicron infected cells compared to other variants.

The lack of syncytia formation led the authors to hypothesise that cell membrane fusion through TMPRSS2 was impaired, which would suggest entry route switching. They found that pseudotype infections (HIV expressing SARS-CoV-2 spike protein) of Omicron were reduced in cells expressing high levels of TMRPSS2, but increased in HEK cells that only support endosomal entry. By using the protease inhibitor Camostat to block TRMPSS2 and prevent cell surface fusion, and E64d to block cathepsins to prevent endosomal fusion, they determined that Omicron prefers the endosomal fusion to the cell surface fusion entry route.


  • In-vitro lung epithelial cell data would need to be corroborated with patient data showing the reduction in lung epithelial function with Omicron

  • Authors also need more replicates in figure 6 to rule out the possibility of false positives and false negatives.


​SARS-CoV-2 Omicron became a variant of concern in mid-November when it was first isolated in South Africa and quickly became the primary SARS-CoV-2 variant in several nations. Identifying the mechanisms that distinguish Omicron from other variants will lead us closer to understanding the more rapid spread of Omicron and to determining how to treat the COVID-19 disease that results from it.


Reviewed by Luisanna Pia as part of the cross-institutional journal club of the Immunology Institute of the Icahn School of Medicine, Mount Sinai, the Kennedy Institute of Rheumatology and the Oxford Centre for Immuno-Oncology  (OXCIO) (University of Oxford, GB) and Karolinska Institute’s Center for Infectious Medicine (CIM) & Center for Molecular Medicine (CMM).

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