SARS-CoV-2 ORF3b is a potent interferon antagonist whose activity is further increased by a naturally occurring elongation variant

Authors: Yoriyuki Konno et al.

Link to paper: https://www.biorxiv.org/content/10.1101/2020.05.11.088179v1.full.pdf


Journal/ Pre-Print: bioRxiv

Tags: Immunology/Immunity, Bioinformatics

Research Highlights 

1. Truncated ORF3b, encoded by SARS-CoV-2 and SARS-CoV-2-related viruses from bats and pangolins, suppresses the induction of type I interferon more efficiently than ORF3b from SARS-CoV and its orthologs.

2. The anti-IFN activity of ORF3b depends on the length of its C-terminus.

3. A natural elongation variant of SARS-CoV-2 ORF3b isolated from two patients showed a stronger suppression of interferon induction than wildtype SARS-CoV-2 ORF3b.

Summary

The authors show that SARS-CoV2 and close relatives, isolated from bats and pangolins, have a truncated ORF3b protein in comparison to SARS-CoV. They assess IFN-β production in 293 cells overexpressing ORF3b constructs upon stimulation with a classical RNA stimulus (Sendai Virus). They find the truncated ORF3b encoded by SARS-CoV-2 (22 aa) suppresses IFN-β induction more efficiently than the full-length SARS-CoV ortholog (~153 aa). Interestingly, extension of SARS-CoV2 ORF3b by removal of a premature stop codon enhances its ability to antagonise IFN-β induction. Finally, SARS-CoV2 isolates from two severe COVID-19 cases were shown to express the extended ORF3b which shows increased IFN-β antagonism. The authors speculate this might enhance the virus’s pathology.

Impact for SARS-CoV2/COVID19 research efforts

Understand the immune response to SARS-CoV2/COVID19

Study Type

● In silico study / bioinformatics study

● In vitro study

● Patient Case study

Strengths and limitations of the paper

Novelty: the anti-IFN activity of ORF3b depends on the length of its C-terminus; a natural elongation variant of SARS-CoV-2 ORF3b was isolated from two patients with severe disease.

Standing in the field: Previous studies on SARS-CoV and related viruses demonstrated that ORF3b has the ability to inhibit IFN-I production; poor induction of a type I interferon (IFN-I) response distinguishes COVID-19 from SARS in terms of immune responses.

Appropriate statistics: Yes

Viral model used: SeV (strain Cantell, clone cCdi; accession no. AB855654)

Translatability: Strains of SARS-CoV2 with ORF3b mutation could potentially be an indicator of disease severity.

Main limitations:

1) Cells were stimulated to produce IFN with SeV, not the actual virus.

2) The induction of interferon was measured only by a luciferase assay, lacking protein and other level evidence.

3) The expression of SARS-CoV-2 ORF3b constructs (119*, 155*) protein are lower than WT, therefore it’s difficult to draw a conclusion from the interferon induction data

4) The relationship between the elongation ORF3b variant and the severity of the disease in patients is not clear