Potential therapy candidates for patients infected with the SARS-CoV-2 Omicron variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) has been shown to cause milder symptoms of the coronavirus disease 2019 (COVID-19) when compared to previous SARS-CoV-2 variants.

A new study published in the bioRxiv* preprint server discusses why Omicron variant infections cause mild disease and several promising therapeutic candidates that have been proposed for the treatment of patients infected with the Omicron variant.

Study: SARS-CoV-2 Omicron variant virus isolates are highly sensitive to interferon treatment. Image Credit: kittpong053 / Shutterstock.com

Omicron variant infection

One of the ways in which the human body combats viral infections is through an interferon (IFN) response. IFNs create conditions that restrict viral replication and target the viral antigens to be neutralized by antibodies.

During SARS-CoV-2 infection, the host generates an IFN response. The SARS-CoV-2 Delta variant effectively inhibits the host cell IFN response; however, the Omicron variant is less effective in inhibiting this immune response.

Currently, COVID-19 vaccine-conferred immunity is weak in protecting against the Omicron variant. Even so, the Omicron variant appears to be less pathogenic as compared to other SARS-CoV-2 variants of concern. Furthermore, the Omicron variant shows a lower capacity to replicate in the lower respiratory tract.

In vitro study

In the current study, a SARS-CoV-2 Delta isolate and two Omicron isolates of Omicron 1 and Omicron 2 were used. The intestinal cell line of Caco-2 and the lung cell line of Calu-3 were infected with the SARS-CoV-2 isolates.

The infectious titer was determined 24 hours post-infection. Total and phosphorylated signal transducer and activator of transcription (STAT1) levels were determined through immunoblotting. STAT1 phosphorylation is an important event during IFN signaling; therefore, high phosphorylated STAT1 levels indicate increased IFN signaling.

A549 lung cells expressing the angiotensin-converting enzyme (ACE2) receptor and transmembrane serine protease 2 (TMPRSS2) were also used due to their ability to be infected by SARS-CoV-2. To this end, A549 cells were infected with Delta, Omicron 1, and Omicron 2 variants. The number of infected cells was determined by immunofluorescence staining.

The infection experiments were repeated with cells in which melanoma differentiation-associated protein 5 (MDA5) and retinoic acid-inducible gene I (RIG-I) were knocked out. MDA5 and RIG-I are the pattern recognition receptors that mediate the host cell IFN response in virus-infected cells. Without these receptors, the cells will not be able to generate an IFN response after viral infection.

The production of IFN α/β was measured using HEK-Blue IFNα/β reporter cells. To evaluate the antiviral effect of IFNs, the dose-response curves of IFNα, IFNβ, and IFNγ were estimated in Caco-2 and Calu-3 cells.

All IFNs were added to the cells, which were then infected with the SARS-CoV-2 variants. The inhibition rate was evaluated 24 hours (Caco-2) or 48 hours (Calu-3) post-infection by staining the spike protein. The antiviral effect of IFNβ was also tested in combination with nirmatrelvir, which is the antiviral agent in paxlovid, and remdesivir in Caco-2 cells.

Omicron isolates and interferon signaling

The two SARS-CoV-2 Omicron isolates replicated to lower titers than the Delta isolate in Caco-2 and Calu-3 cells. The Omicron isolates also induced elevated STAT1 phosphorylation, thereby demonstrating their ability to increase IFN signaling, whereas the Delta isolate antagonized IFN signaling.

Similarly, in A549 cells, the Omicron variants had lower infection capacities as compared to the Delta isolte. This difference in infection capacity disappeared to a large extent when MDA5 and RIG-I were depleted.

In the absence of MDA5 and RIG-I, Omicron variants replicated as well as the Delta variant. Taken together, these experiments demonstrate that the Omicron variants have lower infection capacity because they are inhibited by the host cell IFN response.

The supernatants of Omicron -infected RIG-I-knock out cells had higher interferon activity than the supernatants of Omicron -infected MDA5-knock out cells. Thus, MDA5 primarily induces an IFN response in SARS-CoV-2-infected cells.

The Omicron isolates were sensitive to IFN treatment. Further, IFNβ, in combination with nirmatrelvir and remdesivir, showed enhanced antiviral effects.

Conclusions

The SARS-CoV-2 Omicron variant appears to be less effective than the Delta variant in antagonizing the host cell IFN response, a property that appears to be unique to the Omicron variant.

Until now, there are mixed reports on the outcomes in COVID-19 patients treated with different IFNs. The current study presents IFNs as a promising option for the treatment of patients infected with the Omicron variant.

*Important notice

bioRxiv 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.

Journal reference:
Dr. Shital Sarah Ahaley

Written by

Dr. Shital Sarah Ahaley

Dr. Shital Sarah Ahaley is a medical writer. She completed her Bachelor's and Master's degree in Microbiology at the University of Pune. She then completed her Ph.D. at the Indian Institute of Science, Bengaluru where she studied muscle development and muscle diseases. After her Ph.D., she worked at the Indian Institute of Science, Education, and Research, Pune as a post-doctoral fellow. She then acquired and executed an independent grant from the DBT-Wellcome Trust India Alliance as an Early Career Fellow. Her work focused on RNA binding proteins and Hedgehog signaling.

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