Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment

Brief Bioinform. 2021 Mar 22;22(2):1430-1441. doi: 10.1093/bib/bbaa417.


The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.

Keywords: COVID-19; SARS-CoV-2; coronavirus; data integration; drug repositioning; drug targeting; multi-layer network analysis; unified knowledge space; virus–host interaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / therapeutic use*
  • COVID-19 / genetics
  • COVID-19 / physiopathology
  • COVID-19 / virology
  • COVID-19 Drug Treatment*
  • Genes, Viral
  • Humans
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification
  • Transcriptome


  • Antiviral Agents