SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes

• Published in: Journal of proteome research Vol. 19; no. 11; pp. 4275 - 4290
• Main Authors: Sirpilla, Olivia, Bauss, Jacob, Gupta, Ruchir, Underwood, Adam, Qutob, Dinah, Freeland, Tom, Bupp, Caleb, Carcillo, Joseph, Hartog, Nicholas, Rajasekaran, Surender, Prokop, Jeremy W
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 06-11-2020
• Subjects: Betacoronavirus; Coronavirus Infections - genetics; Coronavirus Infections - metabolism; Coronavirus Infections - virology; COVID-19; Databases, Genetic; Gene Expression Profiling; Host-Pathogen Interactions; Humans; Pandemics; Pneumonia, Viral - genetics; Pneumonia, Viral - metabolism; Pneumonia, Viral - virology; Proteome - genetics; Proteome - metabolism; Reviews; Ribosomes - genetics; Ribosomes - metabolism; Ribosomes - virology; SARS-CoV-2; Transcriptome; Viral Proteins; COVID-19; nucleocapsid; SARS-CoV-2; risk factors; nonsense-mediated decay; proteomics; host interactions; transcriptomics; viral-induced genetics
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.0c00421

SARS-CoV-2 (COVID-19) has infected millions of people worldwide, with lethality in hundreds of thousands. The rapid publication of information, both regarding the clinical course and the viral biology, has yielded incredible knowledge of the virus. In this review, we address the insights gained for the SARS-CoV-2 proteome, which we have integrated into the Viral Integrated Structural Evolution Dynamic Database, a publicly available resource. Integrating evolutionary, structural, and interaction data with human proteins, we present how the SARS-CoV-2 proteome interacts with human disorders and risk factors ranging from cytokine storm, hyperferritinemic septic, coagulopathic, cardiac, immune, and rare disease-based genetics. The most noteworthy human genetic potential of SARS-CoV-2 is that of the nucleocapsid protein, where it is known to contribute to the inhibition of the biological process known as nonsense-mediated decay. This inhibition has the potential to not only regulate about 10% of all biological transcripts through altered ribosomal biology but also associate with viral-induced genetics, where suppressed human variants are activated to drive dominant, negative outcomes within cells. As we understand more of the dynamic and complex biological pathways that the proteome of SARS-CoV-2 utilizes for entry into cells, for replication, and for release from human cells, we can understand more risk factors for severe/lethal outcomes in patients and novel pharmaceutical interventions that may mitigate future pandemics.