Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site
biochemistry bioinformatics molecular biology proteomics structural biology virology
Authors: Davidson et al.
Link to paper: https://www.biorxiv.org/content/10.1101/2020.03.22.002204v1
Journal/ Pre-Print: BioRxiv
Tags: Biochemistry, Proteomics, Transcriptomics, Structural Biology, Virology, Molecular Biology
1. Integrated transcriptome and proteome analysis of purified SARS-CoV-2 grown in Vero E6 cells using Oxford Nanopore MinION and Tandem Mass Spectrometry (MS).
2. Identification of viral transcripts (subgenomic mRNAs), as well as corresponding proteins and numerous phosphorylation sites within critical viral proteins.
3. In vitro evidence of a cell passage-induced deletion in the S glycoprotein that removes the furin-like cleavage site at the S1-S2 boundary and is predicted to affect protein cleavage, tropism and infectivity.
In vitro experimental evidence to understand the transcriptome and proteome of a SARS-CoV-2 isolate grown in cell culture. This was the second UK strain isolated. A deletion of the furin-like cleavage site in cell culture provides experimental evidence for mutation of the virus. The SARS-CoV-2 genome can naturally undergo deletions and rearrangements under selective pressure which can have implications for developing immunity and identifying vaccine and therapeutic targets.
Impact for SARS-CoV2/COVID19 research efforts
Understand the virology and/or cell biology of SARS-CoV2/COVID19
· In vitro study
· In silico study / bioinformatics study
Strengths and limitations of the paper
Novelty: One of the first characterisations of the transcriptome and proteome of SARS-CoV-2, and first publication of isolation of a UK strain.
Standing in the field: Consistent with expected findings.
Appropriate statistics: Not Applicable
Viral model used: SARS-CoV-2 UK isolate 2
Translatability: These results could suggest new targets for antiviral drug development. The authors mention the potential for clinically licenced kinase inhibitors against the numerous phosphorylation sites on viral proteins.
Main limitations: Needs to be repeated with other isolates. The high base-call error rate of Oxford Nanopore MinION sequencing could lead to sequencing artefacts which cannot be accounted for in downstream corrections.