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.


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.

Consider installing the browser extension GIX for retrieving human gene information anywhere on this website by double-clicking on its symbol or immediately next to the symbol on report tables.


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.



Start:266Length (BP):13203

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).


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.


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

Human cell

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

Cell infected with SARS-CoV-2

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 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.