7 results on '"Brendan Rodoni"'
Search Results
2. Viroid-infected Tomato and Capsicum Seed Shipments to Australia
- Author
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Fiona Constable, Grant Chambers, Lindsay Penrose, Andrew Daly, Joanne Mackie, Kevin Davis, Brendan Rodoni, and Mark Gibbs
- Subjects
pospiviroid ,viroid ,PSTVd ,tomato ,capsicum ,seed ,trade ,detection ,Microbiology ,QR1-502 - Abstract
Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 × 10−5 (~1 in 16,000; CI 5 × 10−6 to 2.5 × 10−4) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion.
- Published
- 2019
- Full Text
- View/download PDF
3. The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia
- Author
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Wycliff M. Kinoti, Fiona E. Constable, Narelle Nancarrow, Kim M. Plummer, and Brendan Rodoni
- Subjects
Ilarvirus ,Prunus ,amplicon high-throughput sequencing ,Apple mosaic virus (ApMV) ,Prune dwarf virus (PDV) ,genetic diversity ,Microbiology ,QR1-502 - Abstract
Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries.
- Published
- 2018
- Full Text
- View/download PDF
4. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses
- Author
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Linda Zheng, Brendan Rodoni, and Solomon Maina
- Subjects
0106 biological sciences ,0301 basic medicine ,Potyvirus ,lcsh:QR1-502 ,Genome, Viral ,01 natural sciences ,Virus ,lcsh:Microbiology ,Article ,Plant Viruses ,Cucumber mosaic virus ,03 medical and health sciences ,plant virus ,Virology ,Plant virus ,Multiplex polymerase chain reaction ,Pea early browning virus ,diagnostics ,genome ,Uncategorized ,Plant Diseases ,biology ,Mosaic virus ,Australia ,Peas ,food and beverages ,high-throughput sequencing ,High-Throughput Nucleotide Sequencing ,Bean yellow mosaic virus ,Amplicon ,biology.organism_classification ,crops ,030104 developmental biology ,Infectious Diseases ,Metagenomics ,010606 plant biology & botany - Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of, Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10−8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
- Published
- 2021
5. Field Verification of an African Swine Fever Virus Loop-Mediated Isothermal Amplification (LAMP) Assay During an Outbreak in Timor L’este
- Author
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Grant Rawlin, Felisiano da Conceição, Brendan Rodoni, Stacey E. Lynch, Joanita Bendita da Costa Jong, Dianne E. Phillips, Shani Wong, Peter T. Mee, and Kim J O'Riley
- Subjects
0301 basic medicine ,Male ,Timor leste ,Timor L’este ,040301 veterinary sciences ,Swine ,Timor-Leste ,lcsh:QR1-502 ,Loop-mediated isothermal amplification ,Positive control ,Real-Time Polymerase Chain Reaction ,African swine fever virus ,Sensitivity and Specificity ,lcsh:Microbiology ,Virus ,Article ,Disease Outbreaks ,0403 veterinary science ,03 medical and health sciences ,LAMP ,Virology ,Animals ,Viremia ,African Swine Fever ,Uncategorized ,biology ,Outbreak ,04 agricultural and veterinary sciences ,Serum samples ,biology.organism_classification ,African Swine Fever Virus ,colourmetric LAMP ,qPCR ,030104 developmental biology ,Infectious Diseases ,Real-time polymerase chain reaction ,Molecular Diagnostic Techniques ,Female ,ASFV ,Nucleic Acid Amplification Techniques - Abstract
Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor L&rsquo, este. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.
- Published
- 2020
- Full Text
- View/download PDF
6. Viroid-infected Tomato and Capsicum Seed Shipments to Australia
- Author
-
Andrew Daly, Kevin Davis, Fiona E. Constable, Grant A. Chambers, Mark J. Gibbs, Brendan Rodoni, Lindsay Penrose, and Joanne Mackie
- Subjects
0106 biological sciences ,0301 basic medicine ,Viroid ,lcsh:QR1-502 ,detection ,Transportation ,pospiviroid ,tomato ,01 natural sciences ,lcsh:Microbiology ,Columnea latent viroid ,Article ,law.invention ,Plant Viruses ,03 medical and health sciences ,Solanum lycopersicum ,law ,Virology ,Plant virus ,Quarantine ,Tomato seed ,Potato spindle tuber viroid ,Phylogeny ,Plant Diseases ,biology ,viroid ,Australia ,Commerce ,PSTVd ,biology.organism_classification ,Viroids ,Horticulture ,030104 developmental biology ,Infectious Diseases ,Pepper chat fruit viroid ,Pospiviroid ,Seeds ,RNA, Viral ,capsicum ,seed ,trade ,010606 plant biology & botany - Abstract
Pospiviroid species are transmitted through capsicum and tomato seeds. Trade in these seeds represents a route for the viroids to invade new regions, but the magnitude of this hazard has not been adequately investigated. Since 2012, tomato seed lots sent to Australia have been tested for pospiviroids before they are released from border quarantine, and capsicum seed lots have been similarly tested in quarantine since 2013. Altogether, more than 2000 seed lots have been tested. Pospiviroids were detected in more than 10% of the seed lots in the first years of mandatory testing, but the proportion of lots that were infected declined in subsequent years to less than 5%. Six pospiviroid species were detected: Citrus exocortis viroid, Columnea latent viroid, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato chlorotic dwarf viroid and Tomato apical stunt viroid. They were detected in seed lots exported from 18 countries from every production region. In many seed lots, the detectable fraction (prevalence) of infected seeds was estimated to be very small, as low as 6 ×, 10&minus, 5 (~1 in 16,000, CI 5 ×, 6 to 2.5 ×, 4) for some lots. These findings raise questions about seed production practices, and the study indicates the geographic distributions of these pathogens are uncertain, and there is a continuing threat of invasion.
- Published
- 2018
7. Updating the Quarantine Status of Prunus Infecting Viruses in Australia
- Author
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Narelle Nancarrow, AL Dann, Fiona E. Constable, Wycliff M. Kinoti, and Brendan Rodoni
- Subjects
0106 biological sciences ,0301 basic medicine ,Apple mosaic virus ,biology ,metagenomic high-throughput sequencing ,viruses ,lcsh:QR1-502 ,Prune dwarf virus ,biology.organism_classification ,01 natural sciences ,lcsh:Microbiology ,Virus ,03 medical and health sciences ,Horticulture ,Prunus ,030104 developmental biology ,Infectious Diseases ,Hop stunt viroid ,prunus ,Virology ,Prunus necrotic ringspot virus ,Plant virus ,Peach latent mosaic viroid ,010606 plant biology & botany - Abstract
One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.
- Published
- 2020
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