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.
Journal/ Pre-Print: bioRxiv
Tags: Immunology/Immunity, Bioinformatics
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.
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
● 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.
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