Study suggests SARS-CoV-2 Omicron variant spike mediated immune escape and tropism shift

By Dr. Ramya Dwivedi, Ph.D.Jan 21 2022Reviewed by Aimee Molineux

An interesting study provides in-depth research into the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant's biological properties and its behavior within cell types and to antibodies.

The study highlights how Omicron gained immune evasion while compromising on key pathways - leading to reduced pathogenicity.

*Important notice: Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

The study showed that the Omicron spike binds to its receptor with enhanced affinity and yet evades vaccine-elicited neutralizing antibodies. While the second vaccine dose effects waned with time, a booster mRNA vaccine increased and broadened the neutralization of Omicron.

This study is currently available on the ResearchSquare* preprint server.

Background

The new SARS-CoV-2 variant, Omicron, first detected in South Africa, has the highest number of mutations observed of any variant so far. There are over 30 mutations in the spike protein, which binds to the angiotensin-converting enzyme 2 (ACE-2) of the host cell to gain entry.

Previous mutations in the Alpha and the Delta variant spike protein conferred the virus efficient cell-cell fusion kinetics. The mutations had increased 1) the S1/S2 cleavage of the spike protein (S1 and S2 are spike subunits) and 2) the syncytia formation; both of which are key to pathogenesis. Localized cell-to-cell infection, is facilitated by syncitium formation.

Omicron also has mutations in these regions, thuswas predicted to be highly infectious and pathogenic. However, recent data on Omicron shows that it is highly transmissible, rapidly increasing the infection cases, with re-infections and vaccine ‘breakthroughs,’ possibly evading vaccine-induced antibodies, yet with reduced severity

Omicron spike has enhanced binding affinity for ACE2

Using biolayer interferometry (BLI), the researchers demonstrated that the Omicron receptor-binding domain (RBD) has a higher affinity for its receptor ACE2 - a 2-2.5 fold relative to the Wuhan-Hu-1 RBD. Dampening as well as additional electrostatic interactions between the Omicron RBD and ACE2 strengthen the binding relative to the ancestral isolate and the Delta variant. The researchers noted that this enhanced binding affinity may be a factor in the enhanced transmissibility of Omicron relative to previous variants.

This study showed that the Omicron spike confers significant evasion of the vaccine-elicited neutralizing antibodies. This is dramatically more for the ChAdOx-1 versus the BNT162b2 vaccine sera. This observation is supported by a UK study of vaccine effectiveness.

Omicron’s evasion of neutralizing activity

Omicron is reported to evade therapeutic monoclonal antibody therapy. The researchers conducted both modeling and experimental studies. Monoclonal antibodies casivirimab and imdevimab neutralized the Delta variant; the combination of the two was highly potent against the Delta variant. However, there was a complete loss of neutralizing activity against Omicron - either alone or in combination.

Omicron and vaccination

Obtaining longitudinal serum samples from doubly vaccinated (either BNT162b2 or ChAdOx-1 vaccines) individuals, the researchers tested the ability of the vaccine-elicited antibodies in the serum to neutralize Omicron. They found that >/= 10-fold loss in neutralization against Omicron compared to Delta. In the case of ChAdOx-1 vaccinated individuals, there was no detectable neutralization.

However, when the third dose was administered, a substantial increase (>10-fold) in neutralization against both Delta and Omicron was observed in the study. Thus, the third vaccination promisingly provides an increased breadth of responses as well as titers. mRNA 1273 vaccine and Coronavac also elicited similar responses.

Poor neutralizing activity to Omicron post-vaccination is observed in developing countries or low-income settings where ChAdOx-1 or Coronavac are administered. This may contribute to higher infection rates and severe disease.

Not only does the vaccine rescue and broadly neutralize Omicron, but the study also showed that the antiviral polymerase inhibitor drugs - remdesevir and molnupiravir, retain efficacy against Omicron.

Omicron spike dependence for cell entry

Mutations in Omicron are predicted to favor the spike S1/S2 cleavage. Despite this, the spike protein is less efficiently cleaved in Omicron virions as compared to Delta virions.

The researchers tested using primary human nasal epithelial 3D cultures (hNEC), Calu-3 lung cells, CaCo-2, HeLa cells, and VeroE6 ACE3/TMPRSS2 cells. Cells known to express endogenous TMPRSS2 had more replication of the Delta variant than Omicron. The TMPRSS2 is a member of the Type II Transmembrane Serine Protease and is a cofactor for SARS-CoV-1, MERS, and SARS-CoV-2.

Also, the Omicron spike was inefficiently cleaved in virions compared to Delta.

This study demonstrated that these replication differences between the variants led to differences in the viral entry efficiency.  Using spike pseudotyped virus (PV) entry assays, the researchers mapped these differences and narrowed them to the inefficient use of the cellular protease TMPRSS2 by Omicron spike protein to gain cell entry.

The TMPRSS2 mediates cell entry via plasma membrane fusion. Instead, Omicron depended on the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike.

The limitation of the Omicron pseudotyped virus in specific cell types correlated with higher expression of TMPRSS2 (cellular mRNA). This explained how the knockdown of TMPRSS2 impacted Delta variant entry to a greater extent but not Omicron’s entry.

This is further supported by how drug inhibitors that target specific entry pathways demonstrated that the Omicron spike inefficiently used the cellular protease TMPRSS2. Because the Omicron fails to achieve a suboptimal S1/S2 cleavage and utilize the TMPRSS2, syncytium formation by the Omicron spike is observed to be dramatically impaired compared to the Delta spike.

Omicron’s shift in cellular tropism

Impaired entry efficiency was clearly observed in the primary 3D lower airway organoids and gall bladder organoids and in Calu-3 lung cells.

Due to its non-dependence on TMPRSS2 expressing cells, Omicron appears to have shifted cellular tropism away from lower respiratory and GI tracts where the cells are enriched with these TMPRSS2-rich cells. It has compromised its ability to mediate entry in cells expressing TMPRSS2.

Though the study is conducted in vitro, the organoid systems and human nasal epithelial cultures used here are primary human tissues. The researchers call for further in vivo studies to understand the impact on an infected animal.

Conclusion

Overall, this study provides insight into how Omicron appears to significantly evasion from neutralizing antibodies but succumbing to the antiviral drugs targeting the polymerase. Importantly, the dose vaccination waning is mitigated by the third dose mRNA vaccination that also increased and broadened neutralization of Omicron for a short period.

Significantly the researchers explored the biological properties of Omicron to understand its ‘spike-mediated immune evasion, ACE2 binding interactions, and cellular entry pathways that dictate tissue tropism.’ Detailing the effects of monoclonal antibodies, drugs, inhibitors, and pathways, this study is pivotal and timely.

*Important notice: Research Square publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.