Outbreak response using high-throughput sequencing of plant samples


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Product Description

In an outbreak situation in crops, it is necessary to obtain quickly a good overview of the viruses that may be involved. Only in this way can the right measures be taken to safeguard crop production immediately but also in the long term. High-throughput sequencing (HTS) and bioinformatics analysis of samples offer a global analysis of the phytosanitary status of plants and the rapid and precise identification of pathogens. This service package offers the individual analysis of three plant samples by HTS to ensure a reliable detection of the potentially involved viruses in an outbreak situation.
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Analysis of three individual samples in an outbreak situation, covering all steps of a workflow - from DNA/RNA extraction, state of the art library preparation, sequencing on Illumina platforms and comprehensive bioinformatics analysis.

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1 950,00 €
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Comments (2)

  • n.salem@ju.edu.jo's picture

    Cucurbits are one of the major vegetable crops grown in Jordan. Several pathogenic agents are known to infect cucurbits including fungi, bacteria, nematodes, phytoplasmas and viruses. Recently, during field surveys in Amman, Al-Jafr and Al-Mafraq regions, where cucurbits are highly cultivated, in particular cucumber, squash, melon and watermelon, we have noticed increasing numbers of cucurbit plants showing virus-like symptoms characterized by mosaic, mottling, stunting, stem necrosis and fruit malformation, with high impact on production and marketing value of the crop. The type of symptoms and the pattern of disease distribution in the affected fields suggested a viral etiology. In Jordan, about 10 viruses have been reported to infect cucurbits including Squash leaf curl virus (SLCV), Watermelon chlorotic stunt virus (WCSV), Zucchini yellow mosaic virus (ZYMV), Cucumber vein yellowing virus (CVYV), Watermelon mosaic virus-2 (WMV-2), Cucumber mosaic virus (CMV), Squash mosaic virus (SqMV), Cucurbit yellow stunting disorder virus (CYSDV), Cucurbit chlorotic yellows virus (CCYV) and Cucurbit aphid-borne yellows virus (CABYV). To identify the potential agent(s) causing the observed symptoms, about 240 leaf samples from symptomatic and asymptomatic plants were collected and tested for Cucumber green mottle mosaic virus (CGMMV) and ZYMV by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). Furthermore, representative samples from every field were subjected to total RNA and DNA extraction and tested by PCR-based assay using specific primers for CABYV, CGMMV, CYSDV, CVYV, SLCV, Tomato leaf curl New Delhi virus (TLCNDV) and degenerate primers for begomoviruses. These preliminary investigations revealed virus infections in only a few samples, opening the question of possible infection(s) with novel viruses.
    Recently, High-Throughput Sequencing (HTS) has been broadly used for virus discovery to resolve the disease etiology in many agricultural crops. However, HTS facilities and bioinformatics platforms are not available in Jordan and it would be hard to find financial support to carry out or apply for HTS services whether in Jordan or abroad. Therefore, we are submitting a proposal in the context of the European Virus Archive-Global (EVAg) project, to apply to the EVAg-TNA initiative and perform a virus-discovery analysis of our samples to investigate the presence of (unknown) viruses possibly involved in the observed cucurbit disease. Beside being of high scientific relevance, the results may eventually support initiatives to counteract the disease agent(s) and preserve cucurbits production and food security in different regions of Jordan.

    Aug 22, 2022
  • hilbagi's picture

    Globally, cereals are chiefly cultivated crops that are a crucial source of food and nutrition for human consumption and feed for farm animals. Among the cereal species, maize is one of the most important cereals and is third following wheat and barley, with 8 500 000 tons of production in Turkey. Recently, global climate changes have increased the number of abiotic stress factors and biotic agents, such as pathogens. Among these pathogens, viruses have an enormous impact on crop yield, grain quality, and economic viability in the cereal industry as well as causing severe crop losses in epidemic years. Consequently, the populations of insect vectors and disease incidences have increased in maize crops, reducing yield and quality in recent years. Thus, maize production is at risk for local and systemic diseases. Our observations in the maize fields in the Trakya region of Turkey indicated increased symptoms, such as stripe mosaic, mottle, systemic deformations with reasonably small, formless seeds, and typically virus-like symptoms. In addition, we also observed the typical symptoms such as mosaic, yellowing, and chlorosis in common reed (Phragmites austrialis), a widespread perennial grass usually grown in the wetlands in Trakya, Turkey. Reed is also an invasive grass with rapid expansion, especially threatening biodiversity and competing with cultivated plants. The previous studies revealed that the reed plays an important role in virus epidemiology as a reservoir host. In order to investigate the viruses in both maize and reed, we have collected 150 maize and reed samples, including symptomatic samples exhibiting yellowing, stripe mosaic, mottle, and chlorosis and asymptomatic samples from the Trakya region, and tested by ELISA and RT-PCR tests. The results showed the presence of sugarcane mosaic virus (SCMV), maize dwarf mosaic virus (MDMV), Johnson grass mosaic virus (JGMV), and barley yellow dwarf virus-PAV (BYDV-PAV). Moreover, these preliminary investigations pointed out that some symptomatic and asymptomatic maize and reed samples could include novel viruses. Thus, we need to investigate the other economically significant viruses and novel viruses in maize and reed samples in Trakya, Turkey using the HTS. The obtained results would provide the possibility to form control strategies to prevent a virus epidemic. However, HTS facilities and bioinformatic platforms are not available in Turkey, and it is difficult to find financial support to perform the expected studies and apply for HTS services in Turkey and abroad. Therefore, we would like to submit the summarized proposal for the European Virus Archive-Global (EVAg) project to apply to the EVAg-TNA initiative and to perform the known and unknown viruses’ analysis in maize and reed samples on the Illumina platform.

    Jul 14, 2023