A novel high-throughput sequencing approach reveals the presence of a new virus infecting Rosa: rosa ilarvirus-1 (RIV-1)

Vazquez‐Iglesias, Ines; McGreig, Sam; Pufal, Hollie; Robinson, Rebekah J.; Clover, G. R. G.; Fox, Adrian; Boonham, Neil; Adams, Ian

doi:10.1016/j.jviromet.2021.114417

Cited by 7 publications

(6 citation statements)

References 45 publications

(49 reference statements)

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“…Finally, when comparing the costs for sample, library preparation, and sequencing per sample using either MiSeq (Illumina) or MinION flow cell (Oxford Nanopore Technologies), comparable prices can be estimated if using multiplexing of samples. In the case of MiSeq (Illumina) sequencing, the estimated cost is 189 €/sample if sequencing 24 samples in the same run (Vazquez-Iglesias et al, 2022 ). On the other hand, the estimated cost for barcoding and sequencing 12 or 24 samples on one MinION flow cell using cDNA-PCR barcoding kit and including ribodepletion step is 215 €/sample or 170 €/sample, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…In plant pathology, MinION has been successfully used for the detection of bacteria, fungi, and viruses using RNA or DNA sequencing (Chalupowicz et al, 2019 ), plum pox virus and Candidatus liberibacter asiaticus in plant tissue and insect samples (Bronzato et al, 2018 ), and viruses in wheat (Fellers et al, 2019 ) and cassava (Boykin et al, 2019 ). In several studies (Filloux et al, 2018 ; Beddoe et al, 2020 ; Vazquez-Iglesias et al, 2022 ), both, MinION sequencing and Illumina sequencing, were used for virus detection; however, systematic comparison between established Illumina sequencing and nanopore sequencing for the detection of a wide array of viruses with different genome types is still lacking.…”

Section: Introductionmentioning

confidence: 99%

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Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

et al. 2022

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High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology for the first time and 11 plant viruses with different genome organizations. For all samples, sequencing libraries for the MiSeq were prepared from ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) and for MinION sequencing, direct RNA sequencing of totRNA was used. Moreover, for one of the samples, which contained five different plant viruses and a viroid, three additional variations of sample preparation for MinION sequencing were also used: direct RNA sequencing of rRNA-depleted totRNA, cDNA-PCR sequencing of totRNA, and cDNA-PCR sequencing of rRNA-depleted totRNA. Whilst direct RNA sequencing of total RNA was the quickest of the tested approaches, it was also the least sensitive: using this approach, we failed to detect only one virus that was present in a sample at an extremely low titer. All other MinION sequencing approaches showed improved performance with outcomes similar to Illumina sequencing, with cDNA-PCR sequencing of rRNA-depleted totRNA showing the best performance amongst tested nanopore MinION sequencing approaches. Moreover, when enough sequencing data were generated, high-quality consensus viral genome sequences could be reconstructed from MinION sequencing data, with high identity to the ones generated from Illumina data. The results of this study implicate that, when an appropriate sample and library preparation are selected, nanopore MinION sequencing could be used for the detection of plant viruses and viroids with similar performance as Illumina sequencing. Taken as a balance of practicality and performance, this suggests that MinION sequencing may be an ideal tool for fast and affordable virus diagnostics.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

et al. 2022

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“…These studies mostly focused on the identification of the three main viruses: LSV, LMoV, and CMV ( He et al, 2016 ; Jo and Cho, 2018 ; Kim et al, 2012 ; Kwon et al, 2013 ; Lim et al, 2016 ; Niimi et al, 2003 ; Zhang et al, 2015a , 2015b , 2017 , 2022 ; Zhao et al, 2018 ). Advances in these molecular technologies can help clarify plant viral diseases and more effectively determine their etiology; early diagnosis facilitates plant disease management and is essential for successful biosecurity responses ( Aboul-Ata et al, 2011 ; van der Want and Dijkstra, 2006 ; Vazquez-Iglesias et al, 2022 ).…”

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confidence: 99%

“…Moreover, additional time is required for analysis because the sequencing data cannot be applied to further analysis until the entire sequencing process is complete. In terms of diagnostics, the MinION sequencer and Flongle (flow cell dongle) are ideal for single or small numbers of samples in diagnostic settings, providing low sample throughput with data generated in a short time of 24–48 h at a cost suitable for diagnostic laboratories ( Vazquez-Iglesias et al, 2022 ).…”

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confidence: 99%

“…In recent years, ONT has demonstrated success across a wide variety of plant viruses by generating long-read single-molecule sequence data in real time with an innovation in third-generation sequencing technology ( Jain et al, 2015 ; Lewandowski et al, 2019 ; Zhu et al, 2020 ). ONT has been used to detect plant viruses in a variety of plants, including peaches ( Bronzato Badial et al, 2018 ), tomatoes ( Chalupowicz et al, 2019 ), yams ( Filloux et al, 2018 ), potatoes ( Della Bartola et al, 2020 ), wheat ( Fellers et al, 2019 ), cowpea ( Naito et al, 2019 ), cassava ( Boykin et al, 2019 ), Medicago arborea ( Ben Chehida et al, 2021 ), Jasminum officinale ( Amoia et al, 2022 ), grapevine ( Javaran et al, 2021 ), roses ( Vazquez-Iglesias et al, 2022 ), and lamon bean ( Tarquini et al, 2022 ).…”

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confidence: 99%

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Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses

2022

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Lilies (Lilium spp.) are one of the most important ornamental flower crops grown in Korea. Most viral diseases in lilies are transmitted by infected bulbs, which cause serious economic losses due to reduced yields. Various diagnostic techniques and high-throughput sequencing methods have been used to detect lily viruses. According to Oxford Nanopore Technologies (ONT), MinION is a compact and portable sequencing device. In this study, three plant viruses, lily mottle, lily symptomless, and plantago asiatica mosaic virus, were detected in lily samples using the ONT platform. As a result of genome assembly of reads obtained through ONT, 100% coverage and 90.3-93.4% identity were obtained. Thus, we show that the ONT platform is a promising tool for the diagnosis and characterization of viruses that infect crops.

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Vazquez-Iglesias,

Delmiglio,

Ochoa-Corona

et al. 2024

Viral Diseases of Field and Horticultural Crops

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A novel high-throughput sequencing approach reveals the presence of a new virus infecting Rosa: rosa ilarvirus-1 (RIV-1)

Cited by 7 publications

References 45 publications

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach

Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses

Rose

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