Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2

• Published in: PloS one 2020-12, Vol.15 (12), p.e0236304
• Main Authors: Llabrés, Mercè, Valiente, Gabriel
• Format: Article
• Language: English
• Subjects: Alignment; Biology and Life Sciences; Community relations; Computer and Information Sciences; Coronaviridae; Coronavirus - metabolism; Coronavirus Infections - virology; Coronaviruses; COVID-19; COVID-19 - virology; Development and progression; Host Microbial Interactions - physiology; Host-virus relationships; Humans; Infections; Infectious diseases; Integer programming; Linear programming; Medicine and health sciences; Models, Theoretical; Networks; Pandemics; Physiological aspects; Pneumonia, Viral - virology; Programming, Linear; Protein Binding - physiology; Protein interaction; Protein Interaction Maps - physiology; Protein-protein interactions; Proteins; Proteins - metabolism; Public health; SARS-CoV-2 - metabolism; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Software; Spike Glycoprotein, Coronavirus - metabolism; Viral diseases; Viral infections; Viral research; Virus Replication - physiology; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0236304

Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has considerably increased its effort to discover the infection strategies of the new virus. Among the extensive and crucial research that has been carried out in the last months, the analysis of the virus-host relationship plays an important role in drug discovery. Virus-host protein-protein interactions are the active agents in virus replication, and the analysis of virus-host protein-protein interaction networks is fundamental to the study of the virus-host relationship. We have adapted and implemented a recent integer linear programming model for protein-protein interaction network alignment to virus-host networks, and obtained a consensus alignment of the SARS-CoV-1 and SARS-CoV-2 virus-host protein-protein interaction networks. Despite the lack of shared human proteins in these virus-host networks, and the low number of preserved virus-host interactions, the consensus alignment revealed aligned human proteins that share a function related to viral infection, as well as human proteins of high functional similarity that interact with SARS-CoV-1 and SARS-CoV-2 proteins, whose alignment would preserve these virus-host interactions.