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

Mercè Llabrés,Gabriel Valiente

doi:10.1371/journal.pone.0236304

Mercè Llabrés, Gabriel Valiente

Open Access

https://doi.org/10.1371/journal.pone.0236304

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Abstract

MotivationBeside 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.ResultsWe 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.

Highlights

The present outbreak of a coronavirus-associated acute respiratory disease, the COVID-19 pandemic, has forced the scientific community to rapidly analyze the virus-host relationships of the new coronavirus (SARS-CoV-2) human infection
Notice that we have excluded any interactions among the 109 human proteins in the SARS-CoV-1-Human network, as well as any interactions among the 332 human proteins in the SARS-CoV-2-Human network
These host-host interactions do not contribute to improving the quality of the virus-host protein-protein network alignment, they rather introduce noise and, the inclusion of both virus-host and host-host interactions in the SARS-CoV-1-Human and SARS-CoV2-Human networks results in the alignment of four of the SARS-CoV-1 proteins with host proteins (P61019, P06280, Q9Y375, and Q9Y5J7, respectively) instead of SARS-CoV-2 proteins

Summary

Motivation

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

Results

Introduction

Methods

Results and discussion