Research » WP 1.1 Virus identification

Despite large ongoing efforts to identify viruses in humans, animals and the environment, there are still multiple challenges remaining in the identification of novel viruses. These challenges remain both in the wet-lab as well as on the bioinformatical side. On the wet-lab side, divergent viruses can now be identified from an infected sample en masse, but different research groups use different protocols to analyse these samples and prepare them for sequencing. All the current approaches result in relative distributions, which lack (not only clinically important) absolute quantitation. Sample preparation, methods and standardisation are prerequisites for meaningful and comparable work. On the bioinformatical side, the most frequently used similarity-based virus identification approaches are largely limited by available databases, which are incomplete and often poorly annotated. VIROINF (together with the European Virus Bioinformatics Center) aims to set up a multiple-layer database for phages and their hosts (WP 1.2).

VIROINF aims to quantify viruses by four approaches (ESR 11):

  • spiking in known amounts of selected viruses into a sample;
  • developing qPCR assays for a selection of abundant viruses in particular sample sets;
  • counting virus particles using flow cytometric approaches in collaboration with Corina Brussaard from the Netherlands Institute for Sea Research; and
  • NGS-based quantification developed in collaboration with Baseclear.

The novel wet-lab approaches will be combined with newly developed advanced bioinformatical tools to identify viruses from metagenomic datasets (ESR 12), using sequence-dependent and -independent approaches. Motif searches, k-mer frequencies, and genome organisation are de novo approaches that will complement homology-based methods, allowing the detection of known and unknown viruses, yielding a comprehensive detection pipeline of all types of viruses ranging from well-studied human pathogens to completely novel bacteriophages. A range of available tools for taxonomic classification will be combined into a rapid pipeline.

PhD Projects

Main projects:

Side projects:

Journal Articles

Rozwalak, Piotr; Barylski, Jakub; Wijesekara, Yasas; Dutilh, Bas E.; Zielezinski, Andrzej

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces Journal Article

In: Nat Commun, vol. 15, iss. 1, pp. 495, 2024.

Abstract | Links | BibTeX

Luo, Shiqi; Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Ralser, Anna; Luque, Raquel Mejías; Gerhard, Markus; Deng, Li

Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection Journal Article

In: Gut Microbes, vol. 15, iss. 2, pp. 2257291, 2023.

Abstract | Links | BibTeX

Wu, Ling-Yi; Pappas, Nikolaos; Wijesekara, Yasas; Piedade, Gonçalo J.; Brussaard, Corina P. D.; Dutilh, Bas E.

Benchmarking Bioinformatic Virus Identification Tools Using Real-World Metagenomic Data across Biomes Journal Article

In: bioRxiv, 2023.

Abstract | Links | BibTeX

Ru, Jinlong; Mirzaei, Mohammadali Khan; Xue, Jinling; Peng, Xue; Deng, Li

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis Journal Article

In: Gut Microbes, vol. 15, iss. 1, pp. 2192522, 2023.

Abstract | Links | BibTeX

Goettsch, Winfried; Beerenwinkel, Niko; Deng, Li; Dölken, Lars; Dutilh, Bas E.; Erhard, Florian; Kaderali, Lars; von Kleist, Max; Marquet, Roland; Matthijnssens, Jelle; McCallin, Shawna; McMahon, Dino; Rattei, Thomas; van Rij, Ronald P.; Robertson, David L.; Schwemmle, Martin; Stern-Ginossar, Noam; Marz, Manja

ITN -- VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics Journal Article

In: Viruses, vol. 13, no. 5, pp. 766, 2021.

Abstract | Links | BibTeX


Basler, Nikolas; de Graaf, Dirk C.; Smet, Lina De; Matthijnssens, Jelle

The honey bee gut microbiome – a diversity profile of different gut parts and seasons across eight European countries Presentation

Oral presentation at 9th European Congress of Apidology (EurBee9), 20.09.2022, (Best Oral Presentation).

Abstract | BibTeX