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Authors:Arinjay Banerjee et al.,  

Journal/ Pre-Print:bioRxiv 

Tags: Bioinformatics, Cell Biology, Immunology/Immunity, Virology 

Research Highlights 

  1. Pathway analysis of RNA sequencing data from Calu-3 cells infected with SARS-CoV2 shows the changes in cellular and viral transcriptome over the first 12 hours of infection.  

  1. SARS-CoV2 infection induces production of moderate but not maximal levels of IFN- β.  

Summary  

Recent work suggests that SARS-CoV2 does not induce robust IFN responses in human cells. This paper addresses this question by preforming RNA sequencing of Calu-3 cells over the first 12 hours of SARS-CoV2 infection. The authors report moderate IFN and ISG induction from 12 hours post infection. Additionally, pathway enrichment analysis predicted the cellular processes modulated during infection. 

Impact for SARS-CoV2/COVID19 research efforts  

Understand the immune response to SARS-CoV2/COVID19  

Understand the virology and/or cell biology of SARS-CoV2/COVID19 

Study Type  

  • In vitro study 

Strengths and limitations of the paper 

Novelty: Shows changes in viral and cellular transcriptome over the first 12 hours of SARS- CoV-2 infection.  

Standing in the field: This data set tries to address the controversy of whether SARS-CoV-2 induces interferon production by looking over time, rather than at a set time point like many other studies. The authors report a moderate amount of IFN-β is induced at 12hpi. There are known SARS-CoV-2 interferon antagonists; this is at odds with the other conclusion drawn in this study: that SARS-CoV-2 does not antagonise the interferon response. 

Appropriate statistics: yes 

Viral model used:SARS-CoV-2/SB3  

Translatability: None 

Main limitations:  

The authors do not justify the timepoints chosen for this study. There are minimal changes in both cellular and viral transcriptomes before 6 h, as shown in Figure 1. It would be better to include later timepoints rather than all of the early (1, 2, 3 hpi) timepoints. 

In the text the authors state they see high levels of cell death at late time points (quote below) but draw all of their conclusions from their final time point 12 hpiIn addition, they do not explain the choice of using SARS-CoV-2 only at MOI 2, which they describe as a high MOI. 

“High MOI of SARS-CoV-2 produced cytopathic effects (CPE) in Calu-3 cells at later time points, which made it difficult to reliably assess host gene expression relative to unstable levels of house-keeping genes.” 

The paper claims that SARS-CoV2 cannot block interferon generated from exogenous stimuli. However, the authors only treat cells with the RNA stimulus poly I:C. It is possible SARS-CoV2 might be able to block interferon production from other viral sensing pathways (e.g. cGAS-STING pathway). Hence it would be interesting to test if SARS-CoV2 infection inhibited IFN production on transfection of DNA.  

The authors only use a single dose of poly I:C on these cells. The authors conclude that SARS-CoV2 induces less IFN than poly I:C. Dose titration curves are needed to show that neither of these stimuli are saturating IFN production. It is possible at a lower dose of poly I:C SARS-CoV2 may be able to inhibit IFN production.