Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells

Authors:Ravindra et al.

Link to paper: https://www.biorxiv.org/content/10.1101/2020.05.06.081695v1.full.pdf

Journal/ Pre-Print:bioRxiv

Key Words: scRNA-seq, longitudinal, in vitro

Research Highlights 

1. Longitudinal analysis of SARS-COV-2 infected human bronchial epithelial cells (HBECs) by scRNA-Seq.

2. RT-qPCR shows the presence of viral transcripts, which allows discrimination of infected cells and bystander cells.

3. SARS-CoV-2 reprograms the cellular transcriptome of primary infection target - ciliated cells - that had increased gene expression involved in apoptosis, translation initiation and viral gene expression.

Summary

Ravindra et al present longitudinal single-cell RNA-seq analysis of established organoid model that reproduces composition and orientation of respiratory epithelium (HBECs) infected with SARS-CoV-2. They identified ciliated cells as the major target of infection, followed by basal and club cells. They found poor correlation of cell tropism with expression of virus entry receptor ACE2 and implicated proteases CTSL and TMPRSS2. By separating infected and bystander cells, they found that SARS-CoV-2 reprograms the cellular transcriptome as infected ciliated cells had increased gene expression involved in apoptosis, translation initiation and viral gene expression.

Impact for SARS-CoV2/COVID19 research efforts

Understand the immune response to SARS-CoV2/COVID19: they assessed the innate immune response in a longitudinal single-cell approach.

Understand the virology and/or cell biology of SARS-CoV2/COVID19: they determined cell tropism of SARS-CoV-2.

Study Type

· In silico study / bioinformatics study

· In vitro study

Strengths and limitations of the paper

Novelty: Identification of cell tropism and changes along course of infection, novel method to differentiate infected cell types

Standing in the field: The poor correlation between cell tropism with expression of virus entry receptor ACE2 and implicated proteases CTSL and TMPRSS2 is unexpected, but important as a plethora of papers have performed scRNAseq for ACE2/TMPRSS2 expression to predict what cells are likely to be infected. Now it seems this is not the way forward.

Appropriate statistics: Yes, standard analysis methods used and relatively stringent multiple testing corrections applied.

Viral model used: SARS-CoV-2 isolate USA-WA1/2020 used for experimental in vitro infection

Translatability: in vitro studies need to be verified in vivo, longitudinal study helpful but not sure if dpi in vitro reflect dpi in vivo, confirmation of role for IL-6.

Only lower respiratory tract is modelled with HBECs, so ciliated cells are primary site of infection in this area.

Main limitations: in vitro study, protease and determinant for cell tropism and susceptibility remain unidentified.