Oxford Nanopore Sequencing Reveals an Exotic
            <i>Broad bean mottle virus</i>
            Genome within Australian Grains Post-Entry Quarantine

Maina, Solomon; Norton, Stacie; McQueen, V. L.; King, Simon; Rodoni, Brendan

doi:10.1128/mra.00211-22

Cited by 6 publications

(6 citation statements)

References 12 publications

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“…As most plant viral genomes are composed of RNA, RNA sequencing (RNA-Seq) is an example of a highly used metagenomics tool that has gained momentum for both quantifying and mapping transcriptomes and the integrated mining of viral sequences. In plant virology, HTS has largely been adopted as a universal method for the detection and discovery of previously unknown viruses and viroids (Villamor et al, 2019;Maina et al, 2021;Whattam et al, 2021;Lebas et al, 2022;Maina et al, 2022;AlcaláBriseño et al, 2023;Fontdevila Pareta et al, 2023). The RNA-Seq approach involves converting RNA extracts to cDNA and then ligating adaptors to facilitate the pooling of multiple samples for sequencing of tagged DNA.…”

Section: Metagenomics As a Common Rna Sequencing Toolmentioning

confidence: 99%

“…The most effective way to limit the spread of pathogens, such as viruses, is by regulating the movement of plants and plant products through phytosanitary systems (Gullino et al, 2021). HTS has been applied extensively in seed and vegetative propagules virus testing, and its deployment in international phytosanitary border zones could prevent the introduction of damaging viruses into new geographic cropping regions or natural ecosystems (Maliogka et al, 2018;Maina et al, 2021;Bester et al, 2022, Maina et al, 2022.…”

Section: Introductionmentioning

confidence: 99%

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High-throughput sequencing for plant virology diagnostics and its potential in plant health certification

Maina,

Donovan,

Plett

et al. 2024

Front. Hortic.

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High-throughput sequencing (HTS) technologies have revolutionized plant virology through simultaneous detection of mixed viral infections. HTS advances have uncovered and improved understanding of virus biology, ecology, and evolution which is vital for viral disease management. Plant viruses continue to threaten global agricultural productivity and strict quarantine measures are essential to prevent the introduction and spread of virulent viruses around the world. The gradual decrease in HTS operational costs, including improved computational systems and automation through robotics, has facilitated the adoption of this tool for plant diagnostics, including its use in surveillance and quarantine programs. However, the speed of technology advancements and distinct HTS chemistries, laboratory procedures, data management, and bioinformatic analyses have proven challenging. In addition, the lack of viral species reference sequences, compared with the estimated number of distinct viral taxa, makes classification and identification of novel viruses difficult. There is a need for standardized HTS testing, especially within plant health programs. In this review, we consider the application of HTS in plant virology, explore the technical challenges faced and the opportunities for HTS in plant health certification. We propose standards for overcoming current barriers and for ensuring reliable and reproducible results. These efforts will impact global plant health by reducing the risk of introduction and the spread of damaging novel viruses.

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Section: Metagenomics As a Common Rna Sequencing Toolmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High-throughput sequencing for plant virology diagnostics and its potential in plant health certification

Maina,

Donovan,

Plett

et al. 2024

Front. Hortic.

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show abstract

“…Recent advances in high-throughput sequencing (HTS) and bioinformatic analysis have provided considerable opportunities to upgrade virus surveillance for plant health services and virus discovery, so this subject has recently received considerable worldwide attention (Massart et al, 2014;Adams and Fox, 2016;Massart et al, 2017;Pecman et al, 2017;Adams et al, 2018;Villamor et al, 2019;EPPO, 2022;Lebas et al, 2022;AlcalaB riseño et al, 2023;Fontdevila Pareta et al, 2023), including within Australia (Barrero et al, 2017;Piper et al, 2019;Maina et al, 2021;Whattam et al, 2021;Gauthier et al, 2022;Lelwala et al, 2022;Mackie et al, 2022;Maina et al, 2022). Moreover, the cost of HTS is declining at a significant rate due to advances in sequencing technology, so its application as a routine diagnostic tool is becoming increasing attractive (Villamor et al, 2019;Lebas et al, 2022).…”

Section: High Throughput Sequencingmentioning

confidence: 99%

“…However, Illumina produces shorter read lengths and involves a longer turn around time before results become available than thirdgeneration platforms such as Oxford Nanopore Technology (ONT) (Pecman et al, 2022). Also, ONT provides a convenient means of identifying plant viruses (Bronzato-Badial et al, 2018;Ben Chehida et al, 2021;Liefting et al, 2021;Maina et al, 2022;Pecman et al, 2022;Waite et al, 2022). Its ONT direct RNA sequencing approach involves sequencing RNA without the need for prior amplification and it directly reads RNA without the need for reverse transcription (Phannareth et al, 2020).…”

Section: Illumina and Oxford Nanopore Sequencingmentioning

confidence: 99%

Enhancing biosecurity against virus disease threats to Australian grain crops: current situation and future prospects

Maina,

Jones

2023

Front. Hortic.

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Australia is a major grain exporter, and this trade makes an important contribution to its economy. Fortunately, it remains free of many damaging virus diseases and virus vectors found elsewhere. However, its crop biosecurity is under increasing pressure from global ecological, climatic, and demographic challenges. Stringent biosecurity and plant health programs safeguard Australian grain production from damaging virus and virus vector incursions entering via different pathways. These programs formerly relied upon traditional testing procedures (indicator hosts, serology, PCRs) to intercept incoming virus-contaminated plant material. Recently, the integration of rapid genomic diagnostics innovation involving High Throughput Sequencing (HTS) smart tools into sample testing schedules is under exploration to improve virus testing accuracy, efficiency, and cost effectiveness under diverse circumstances. This process includes evaluating deployment of Illumina and Oxford Nanopore Technology shotgun sequencing. It also includes evaluating targeted viral genome HTS and virus vector metabarcoding approaches. In addition, using machine learning and deep learning capacities for big data analyses and remote sensing technologies will improve virus surveillance. Tracking damaging virus variants will be improved by surveillance networks which combine virus genomic-surveillance systems with an interoperable virus database. Sequencing Australian virus specimen collections will help ensure the accuracy of virus identifications based solely on genetic information. Enhancing routine diagnosis and data collection using these innovations will improve post entry virus interception and background virus and vector surveillance. This will help reduce the frequency of new incursions, improve virus management during eradication, containment and other plant health activities, and achieve more profitable Australian grain production.

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“… 272 Nanopore sequencing's portability and flexible throughput make it uniquely adaptable for plant virus detection. 271 It has been used to detect viruses in common economic crops such as potato, wheat, broad bean, 273 lily, 274 and jasmine. 275 For example, nanopore sequencing can distinguish between virus infection and nutrient deficiency in early‐stage wheat growth and accurately identify Wheat streak mosaic virus while revealing variations in its resistance gene Wsm2.…”

Section: Applications Of Nanopore Sequencing In Other Microbial Detec...mentioning

confidence: 99%

Nanopore sequencing technology and its applications

Zheng

Zhou

Ding

et al. 2023

MedComm

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Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third‐generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID‐19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus‐2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID‐19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID‐19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

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Oxford Nanopore Sequencing Reveals an Exotic Broad bean mottle virus Genome within Australian Grains Post-Entry Quarantine

Cited by 6 publications

References 12 publications

High-throughput sequencing for plant virology diagnostics and its potential in plant health certification

High-throughput sequencing for plant virology diagnostics and its potential in plant health certification

Enhancing biosecurity against virus disease threats to Australian grain crops: current situation and future prospects

Nanopore sequencing technology and its applications

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