NFDI4Microbiota

The NFDI4Microbiota consortium consists of well-established institutions researching bacteria, archaea, protozoa, fungi and viruses. These institutions are already supporting scientists researching the SARS-CoV-2 and the COVID-19 outbreak by providing infrastructure, services and expertise. We invite members of the microbiology community to contact us if you need help in analyzing/hosting large data sets or provision of services (info@nfdi4microbiota.de).

Below is a curated selection of infrastructure, services and activities offered by our consortium members and whose purpose is to serve the virology community.

Web services

• VirusTracker, a web platform to visualize a global spread reconstruction of COVID-19 using air travel and viral genomics data (HZI).
• Development of astarget, a web service for the design of Locked Nucleic Acid (LNA) block specific RNA-interactions. It has already been successfully applied to IncRNAs in human, and it is currently been used to probe and disturb relevant interactions in coronaviruses (SYNMIKRO and UMR).
• Access to compute and storage resources for analyses, as well as hosting of several web services (de.NBI Cloud).
• Access to WASP, a versatile web accessible single cell RNA-seq processing platform (JLU Giessen).
• Development of a platform for FAIR data management, including reproducible and scalable automatic data analysis workflows for the investigation of virus-host interactions (JLU Giessen).
• Access to several text mining and (full) genome analysis services on the ZB MED COVID-19 Hub (ZB MED).

Data collection and data sets

• Viral genome sequencing and annotations (UFZ).
• Virus detection and annotation (e.g., in groundwater) (FSU Jena).
• Nanopore sequencing and modification detection (FSU Jena).
• Development of a repository of coronavirus-related literature ready for text mining (ZB MED).

Methods and standard development

• Detection of amino acid changes providing selective benefit to rapidly evolving viruses. This method, applied to SARS-CoV-2, suggests changes linked to adaptation to the human host since the introduction of this virus into a human population (HZI).
• Development of a method for the design of peptides to block the binding sites of proteins (e.g., receptors). This method is currently used to target the coronavirus spike-protein (UMR).
• Understanding virus emergence from animal reservoirs (FSU Jena).
• Analysis of virus-host interaction (UFZ) during infections with human pathogenic viruses (incl. coronaviruses) by dual RNA-seq. Standardized analysis pipelines and tools for data visualization have been developed and can be made available upon request (JLU Giessen).
• Predicting the host of a virus based on the viral genome sequence (FSU Jena).
• Reconstruction of geographic spread paths and putative outbreak source of RNA viruses (HZI).
• Development of Haploflow, a strain-resolved assembler for viromes and samples with multiple viral strains (HZI).
• Development of a method for linear viral epitope detection (HZI).
• Benchmarking overview and workflow (QuasiModo) of tools for analyzing whole genome sequencing data from clinical samples with mixed strain infections of large viruses (HZI).
• Comparative genome and phylogenetic analyses (UFZ).
• Establishment of a fully automated bioinformatic pipeline for virome analysis (UFZ).
• Virome analysis within the MGX software platform (JLU Giessen).
• Development of specific bioinformatics tools to be applied in virology (FSU Jena).
• Identifying RNA structures and functions in viruses (FSU Jena).
• Metadata standardization for coronavirus genomes being deposited in public repositories (UFZ).

Diagnosis and vaccines

• Development of (1) a SARS-CoV-2 diagnostic pipeline and (2) generic pan-virus assays (UFZ).
• Development of a universal vaccine against influenza viruses (HZI).