NFDI4Microbiota

How does the novel coronavirus (SARS-CoV-2) change its genetic material? What other infections do patients suffer from? Are there genetic predispositions to the coronavirus disease 2019 (COVID-19)? A number of genomics researchers are working hard to bring together their expertise and sequencing infrastructure to help manage the COVID-19 pandemic. In order to accelerate research, these activities are now officially combined in the German COVID-19 OMICS Initiative (DeCOI). Scientists from more than 22 institutes are already involved in DeCOI. The NFDI4Microbiota consortium and its members are actively contributing to this initiative.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19), is now a global threat. Knowledge about COVID-19 must thus be extended immediately. Unfortunately, relatively few genome sequences of SARS-CoV-2 are currently publicly available. To improve this situation, NFDI4Microbiota and partner laboratories are offering to assist researchers in sample preparation, genome sequencing and assembly of SARS-CoV-2, as well as in immediate deposition of resulting sequences in public repositories.
The aim is to significantly increase the number of publicly accessible genome sequences of SARS-CoV-2. Further information can be found on the NFDI4Microbiota webpage SARS-CoV-2 genome sequencing. If you are interested in this service, please contact us at covid19-seq@ndfi4microbiota.de.

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 (contact@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).