COVID-19 interactome
BioID-based interactome of the SARS-CoV-2 proteome
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We profiled twenty-seven of twenty-nine proteins from the viral genome. Select one below to view a detailed report or search by a human identifier for viral proteins that detected it.
Summary
Viruses are obligate intracellular parasites, entirely dependent on host cell protein machinery for their replication. Characterizing how the virus that causes COVID-19, SARS-CoV-2, usurps host cell machinery function, while simultaneously disrupting the cellular antiviral response, will both: (i) dramatically improve our understanding of SARS-CoV-2 pathophysiology and; (ii) identify useful drug targets. The SARS-CoV-2 RNA genome codes for at least twenty-nine proteins. Using a technique called BioID, we aim to characterize the virus-host protein-protein interactome in multiple human cell types.
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Genome
The viral genome is a single-stranded RNA approximately twenty-nine kilobases in size. In has fifteen known open-reading frames that encode twenty-nine proteins. The reference sequence for the features below is MN908947.3.
Click an ORF to view details about it.Tap an ORF to view details about it.
ORF1a
Encodes a polyprotein containing eleven non-structural proteins (NSP 1-11). A ribosomal frameshift leads to an alternative transcript ORF1ab that contains the viral polymerase (NSP12) and helicase (NSP13), and three additional non-structural proteins (NSP14-16).
Localization
There are four structual viral proteins (E - envelope, M - membrane, N - nucleocapsid and S - spike) and 25 non-structural proteins. We are localizing these proteins in host cells using immunfluorescence and Gene Ontology (GO) enrichments of proximal proteins detected in BioID experiments. NB: NSP11 was too small for cloning into the BioID system and is not included in this analysis. ORF10 will be completed in the near future.
Hover over a protein to view its localization or over a compartment to view all viral proteins that localize there.Tap a protein to view its localization or a compartment to view all viral proteins that localize there.
- NSP1
- NSP2
- NSP3
- NSP4
- NSP5
- NSP6
- NSP7
- NSP8
- NSP9
- NSP10
- NSP12
- NSP13
- NSP14
- NSP15
- NSP16
- S
- ORF3A
- ORF3B
- E
- M
- ORF6
- ORF7A
- ORF7B
- ORF8
- N
- ORF9B
- ORF14
Interactome
We detected 7 810 total proximity interactions between exogenous viral baits and native human preys. These interactions are amongst 2 242 unique human proteins. NSP12 had the fewest number of interactions (6) and M had the greatest (938). You can view all interactions on our heat map.
Human proteome ≈ 10K proteins
The A549 proteome has not been precisely defined, but typical cellular proteomes consit of approximately ten-thousand proteins.
Viral proteome = 29 proteins
The SARS-Cov-2 genome encodes twenty-nine known proteins, twenty-seven of which were profiled in this study.
Proximity interactome = 2 242 proteins
We detected over 20% of the estimated A549 proteome to be in proximity to at least one of the viral proteins we expressed. The N protein had only six proximity interactions while M had 938 or ~10% of the cellular proteome.
Network
Network view of viral proteins with their (at most) top twenty-five proximity interactions. Viral proteins are in purple and previoulsy reported interactions are shown as orange lines.
Use the mouse to zoom and pan on the network. Shift-click a node to highlight its interaction partners.Pinch to zoom or tap and drag to move the network. Tap a node to highlight its interaction partners.