A. Goesmann, Justus Liebig Universität Gießen
Service center: Bielefeld-Giessen Resource Center for Microbial Bioinformatics – BiGi
Virus infections remain a major threat to human health. RNA viruses are of particular interest, because their replication machinery introduces a high number of nucleotide substitutions. This leads to high variability among the virus genomes which is an essential factor to adapt to changing environmental conditions or to new hosts. The SFB 1021 investigates RNA viruses from different families covering the respiratory viruses human CoV-229E, MERS-CoV, a highly pathogenic H5N1 IV, a seasonal H1N1 IV and RSV, the hemorrhagic fever causing viruses Ebola virus (EBOV), Marburg virus (MARV), Lassa virus (LASV) and Rift Valley fever virus (RVFV), as well as Nipah virus (NIV), Sandfly fever Sicilian virus (SFSV), and hepatitis C virus (HCV). The SFB 1021 is working on three major projects: (i) synthesis and metabolism of viral RNA, (ii) viral factors determining pathogenicity, and (iii) cellular responses to RNA virus infections and viral factors that counteract or help escape these cellular responses.
As part of the SFB 1021, scientists from the Goesmann Lab in Giessen have analyzed high-throughput RNA-Seq data that were taken from the viruses mentioned. They have set up a bioinformatics pipeline that is adjusted to analyze transcriptome changes of virus-host interactions after infection with RNA viruses over time. The RNA-Seq pipeline provides an automated workflow for the joint evaluation of host transcriptome and viral genome data. In addition, the workflow covers over-representation and Gene Set Enrichment Analyses (GSEA) of GO terms, KEGG and REACTOME pathways as well as protein-protein interaction evaluations using the STRING database. As human corona viruses (CoV-229E and MERS-CoV) are an essential part of this study, this pipeline can also be applied for the newly discovered SARS-CoV-2 to unravel transcriptome changes upon virus infection. For the evaluation of huge data sets, scientist can rely on the de.NBI-Giessen cloud.