Featured projects (1)

Project
The VIRTIGATION project, funded by the EU Horizon 2020 R&I programme, aims at developing rapid and lasting solutions to address emerging viral diseases caused by begomoviruses (whitefly-transmitted) and tobamoviruses (mechanically transmitted) on cucurbits and tomato in Northern Europe and the Mediterranean Basin, as well as at increasing knowledge to better control and manage the viral diseases. Project duration: June 2021 - May 2025 #TOLCNDV #TOBRFV #TYLCV

Featured research (14)

Pea necrotic yellow dwarf virus (PNYDV) is a novel nanovirus in Europe, affecting various grain legumes. The impact of PNYDV on nodulation, symbiotic N 2 fixation and yield parameters in faba bean ( Vicia faba L.) was investigated at controlled conditions in the greenhouse (2017), on-farm in natural infection foci (2018, 2019) and in a small-scale field experiment (2020). In the latter, the standard variety ‘Fuego’ was compared with the variety ‘GL Sunrise’ in early and late infections. In addition, the analogous effects for Pea enation mosaic virus (PEMV) were investigated under greenhouse conditions and the naturally occurring virus spectrum was recorded on-farm and in the field experiment. Results showed a much more severe impact of PNYDV than PEMV on nodulation, leghemoglobin status, N 2 fixation and finally yield, especially in early infections. Although ‘GL Sunrise’ was rated for a less symptomatic field performance toward PNYDV than ‘Fuego’, it showed a similar susceptibility in our field experiment where PNYDV was artificially inoculated to individual plants. Further research on the effect of plant varieties on susceptibility toward PNYDV infection and its spread in single or co-infection mainly with PEMV as a function of climate change acting upon their common aphid vector is required.
p>High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of preparing a laboratory for HTS tests within existing quality assurance systems. From nucleic acid extractions to data analysis and interpretation, all of the steps are covered to ensure reliable and reproducible results. These guidelines are relevant for the detection and identification of any plant pest (e.g. arthropods, bacteria, fungi, nematodes, invasive plants or weeds, protozoa, viroids, viruses), and from any type of matrix (e.g. pure microbial culture, plant tissue, soil, water), regardless of the HTS technology (e.g. amplicon sequencing, shotgun sequencing) and of the application (e.g. surveillance programme, phytosanitary certification, quarantine, import control). These guidelines are written in general terms to facilitate the adoption of HTS technologies in plant pest routine diagnostics and enable broader application in all plant health fields, including research. A glossary of relevant terms is provided among the Supplementary Material.</p
High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data
A novel virus with a quadruple genome of negative-sense, single-stranded (ss) RNA was identified by high-throughput sequencing (HTS) in a grass sample from Saxony-Anhalt, Germany, and tentatively called Festuca stripe-associated virus (FSaV). The genome of FSaV consists of four segments and a total of 16,535 nucleotides (nt) which encode seven open reading frames. FSaV shares highest nt identity (between 72.84% to 80.74%) to Iranian wheat stripe virus (IWSV) and rice hoja blanca virus (RHBV). Additionally, pairwise comparisons between the amino acid sequences of the open reading frames on the genome of FSaV and the corresponding ones on the genomes of the members of the Tenuvirus genus showed that FSaV shared 83.17% and 90.85% aa identity to IWSV. Moreover, the non-coding intergenic regions (ncIR) shared only between 49.5% to 60.87% nt identity to the corresponding regions on the IWSV genome. Based on the ICTV species demarcation, the results suggest that FSaV may represent a new species of the genus Tenuivirus. Plastid sequence analysis of the HTS data showed that the original host is a member of the genus Festuca most likely the species Festuca pratensis.
Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.

Lab head

Heiko Ziebell
Department
  • Institute for Epidemiology and Pathogen Diagnostics (Braunschweig)
About Heiko Ziebell
  • Plant virologist, voluntary fire fighter and keen gardener

Members (2)

Ali Pasha
  • Julius Kühn-Institut
Rabia Ilyas
  • Julius Kühn-Institut
P Lüddecke
P Lüddecke
  • Not confirmed yet
Jonas Hartrick
Jonas Hartrick
  • Not confirmed yet