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  1. Article ; Online: Molecular characterisation of a novel sadwavirus infecting cattleya orchids in Australia.

    Tran, Nga T / Campbell, Paul R / Crew, Kathleen S / Geering, Andrew D W

    Archives of virology

    2024  Volume 169, Issue 3, Page(s) 68

    Abstract: The complete genome sequence of a novel sadwavirus infecting cattleya orchids in South East Queensland is described. Isometric virions of c. 27 nm diameter were observed in sap extracts viewed under a transmission electron microscope, and the genome ... ...

    Abstract The complete genome sequence of a novel sadwavirus infecting cattleya orchids in South East Queensland is described. Isometric virions of c. 27 nm diameter were observed in sap extracts viewed under a transmission electron microscope, and the genome sequence of this virus was determined by high-throughput sequencing. The viral genome consists of two RNA components, 5,910 and 4,435 nucleotides (nt) in length, each encoding a long polyprotein, with predicted cleavage sites at H/Y, E/G, Q/S, and Q/G for the RNA1 and T/G for the RNA2 translation products, respectively. RNA2 has an additional small ORF of 684 nt near the 3' untranslated region. Phylogenetic analysis based on an amino acid sequence alignment of the Pro-Pol region suggested that this virus is most closely related to pineapple secovirus A, a member of the subgenus Cholivirus, but warrants classification as a member of a new species because it exhibited no more than 64% amino acid identity in pairwise sequence comparisons. Because of the prominent purple ringspots that were observed on the leaves of some of the plants, we propose the name "cattleya purple ringspot virus" for this virus (suggested species name: "Sadwavirus cattleyacola").
    MeSH term(s) RNA, Viral/genetics ; Phylogeny ; Amino Acid Sequence ; Secoviridae/genetics ; Virion ; Genome, Viral
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2024-03-07
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-024-05980-1
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  2. Article ; Online: A fungal pathogen is unlikely to be the cause of abnormal vertical growth syndrome in macadamia

    Zakeel, Mohamed C. M. / Geering, Andrew D. W. / Akinsanmi, Olufemi A.

    Plant Pathology. 2023 May, v. 72, no. 4 p.731-741

    2023  

    Abstract: Abnormal vertical growth (AVG) in macadamia is a syndrome that reduces flowering and alters tree architecture, resulting in significant yield losses. The epidemiological parameters suggest the cause is probably a biotic agent with the ability to modulate ...

    Abstract Abnormal vertical growth (AVG) in macadamia is a syndrome that reduces flowering and alters tree architecture, resulting in significant yield losses. The epidemiological parameters suggest the cause is probably a biotic agent with the ability to modulate plant hormone production or signalling. To determine if a fungal pathogen is the cause of AVG, we compared the fungal profile of macadamia trees with or without AVG symptoms using conventional culturing and DNA metabarcoding techniques. A diverse range of fungi was isolated from leaf, root and stem samples of macadamia cultivars HAES 344 and A16. The abundance of the isolated fungi was at least three‐fold higher in trees with AVG symptoms than in trees at the non‐AVG site. Similar results were obtained using DNA metabarcoding. Although the fungal genus Sebacina was the most dominant in the DNA metabarcoding, whereas Diaporthe (>40%) was dominant using the culturing techniques, no unique fungal species was consistently associated with all AVG samples. Therefore, we conclude that it is unlikely that the cause of AVG in macadamia is a fungal pathogen.
    Keywords DNA barcoding ; Diaporthe ; Macadamia ; Sebacina ; cultivars ; fungi ; leaves ; pathogens ; plant architecture ; plant hormones ; plant pathology
    Language English
    Dates of publication 2023-05
    Size p. 731-741.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 415941-x
    ISSN 1365-3059 ; 0032-0862
    ISSN (online) 1365-3059
    ISSN 0032-0862
    DOI 10.1111/ppa.13689
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    Z 945: Show issues

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  3. Article ; Online: Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes.

    Vassilieff, Héléna / Geering, Andrew D W / Choisne, Nathalie / Teycheney, Pierre-Yves / Maumus, Florian

    Biomolecules

    2023  Volume 13, Issue 7

    Abstract: ... ...

    Abstract The
    MeSH term(s) Fossils ; Caulimoviridae/genetics ; Tracheophyta ; Plants/genetics ; Genome, Plant ; Phylogeny
    Language English
    Publishing date 2023-07-03
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom13071069
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  4. Article ; Online: Untangling the taxonomy of dahlia mosaic virus.

    Geering, Andrew D W / McTaggart, Alistair R / Teycheney, Pierre-Yves

    Archives of virology

    2022  Volume 167, Issue 11, Page(s) 2325–2329

    Abstract: In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare ... ...

    Abstract In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare as a pathogen compared to a more recently described but unclassified caulimovirus called dahlia common mosaic virus (DCMV). We have undertaken a new set of analyses to test the hypothesis that DCMV represents a new caulimovirus species whose members infect dahlia, but we ultimately reject this hypothesis. A probable sequencing error was identified in the reference genome sequence of DMV, and consequently, we recommend that an alternative virus isolate be nominated as the exemplar for this species. In accordance with the new binomial nomenclatural system, it is proposed that the virus species be called "Caulimovirus dahliae".
    MeSH term(s) Caulimovirus ; Dahlia ; Phylogeny ; Viruses
    Language English
    Publishing date 2022-08-15
    Publishing country Austria
    Document type Journal Article ; Review
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-022-05567-8
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    Ud II Zs.110: Show issues Location:
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  5. Article: Surveillance for Avocado Sunblotch Viroid Utilizing the European Honey Bee (

    Roberts, John M K / Jooste, Anna E C / Pretorius, Lara-Simone / Geering, Andrew D W

    Phytopathology

    2023  Volume 113, Issue 3, Page(s) 559–566

    Abstract: Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection ... ...

    Abstract Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection possible via either the male (pollen) or female gametes. Surveillance for ASBVd across commercial orchards is a major logistical task, particularly when aiming to meet the stringent standards of evidence required for a declaration of pest freedom. As with many fruit crops, insect pollination is important for high avocado yields, and honey bee (
    MeSH term(s) Bees ; Animals ; Plant Diseases/prevention & control ; Plant Viruses ; Viroids/genetics ; Persea ; Pollination
    Language English
    Publishing date 2023-02-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208889-7
    ISSN 1943-7684 ; 0031-949X
    ISSN (online) 1943-7684
    ISSN 0031-949X
    DOI 10.1094/PHYTO-08-22-0295-R
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    Zs.B 698: Show issues Location:
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  6. Article ; Online: Surveillance for Avocado Sunblotch Viroid Utilizing the European Honey Bee (Apis mellifera)

    Roberts, John M. K. / Jooste, Anna E. C. / Pretorius, Lara-Simone / Geering, Andrew D. W.

    Phytopathology®. 2023 Mar., v. 113, no. 3 p.559-566

    2023  

    Abstract: Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection ... ...

    Abstract Avocado is one of the world's fastest growing tropical fruit industries, and the pathogen avocado sunblotch viroid (ASBVd) is a major threat to both production and access to international export markets. ASBVd is seed transmissible, with infection possible via either the male (pollen) or female gametes. Surveillance for ASBVd across commercial orchards is a major logistical task, particularly when aiming to meet the stringent standards of evidence required for a declaration of pest freedom. As with many fruit crops, insect pollination is important for high avocado yields, and honey bee (Apis mellifera) hives are typically moved into orchards for paid pollination services. Exploiting the foraging behavior of honey bees can provide a complementary strategy to traditional surveillance methods. High-throughput sequencing (HTS) of bee samples for plant viruses shows promise, but this surveillance method has not yet been tested for viroids or in a targeted plant biosecurity context. Here, we tested samples of bees and pollen collected from pollination hives in two ASBVd orchard locations, one in Australia, where only four trees in a block were known to be infected, and a second in South Africa, where the estimated incidence of infection was 10%. Using real-time RT-PCR and HTS (total RNA-seq and small RNA-seq), we demonstrated that ASBVd can be confidently detected in bees and pollen samples from hives within 100 m of infected trees. The potential for using this approach in ASBVd surveillance for improved orchard management and supporting market access is discussed.
    Keywords Apis mellifera ; Avocado sunblotch viroid ; avocados ; biosecurity ; exports ; females ; fruits ; honey ; honey bees ; insect pollination ; males ; market access ; monitoring ; orchards ; pathogens ; pests ; pollen ; sequence analysis ; viroids ; Australia ; South Africa ; eDNA ; high-throughput sequencing ; plant viruses
    Language English
    Dates of publication 2023-03
    Size p. 559-566.
    Publishing place The American Phytopathological Society
    Document type Article ; Online
    ZDB-ID 208889-7
    ISSN 1943-7684 ; 0031-949X
    ISSN (online) 1943-7684
    ISSN 0031-949X
    DOI 10.1094/PHYTO-08-22-0295-R
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  7. Article ; Online: Untangling the taxonomy of dahlia mosaic virus

    Geering, Andrew D. W. / McTaggart, Alistair R. / Teycheney, Pierre-Yves

    Arch Virol. 2022 Nov., v. 167, no. 11 p.2325-2329

    2022  

    Abstract: In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare ... ...

    Abstract In this brief note, we review the taxonomic history of dahlia mosaic virus (DMV) and related viruses. DMV is the only officially recognized caulimovirus known to infect dahlia (Dahlia variabilis) plants, although this virus appears to be relatively rare as a pathogen compared to a more recently described but unclassified caulimovirus called dahlia common mosaic virus (DCMV). We have undertaken a new set of analyses to test the hypothesis that DCMV represents a new caulimovirus species whose members infect dahlia, but we ultimately reject this hypothesis. A probable sequencing error was identified in the reference genome sequence of DMV, and consequently, we recommend that an alternative virus isolate be nominated as the exemplar for this species. In accordance with the new binomial nomenclatural system, it is proposed that the virus species be called “Caulimovirus dahliae”.
    Keywords Dahlia mosaic virus ; Dahlia pinnata ; nucleotide sequences ; pathogens ; taxonomy ; viruses
    Language English
    Dates of publication 2022-11
    Size p. 2325-2329.
    Publishing place Springer Vienna
    Document type Article ; Online
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-022-05567-8
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  8. Article: Development of a one-step RT-qPCR detection assay for the newly described citrus viroid VII

    Chambers, Grant A. / Geering, Andrew D.W. / Holford, Paul / Vidalakis, Georgios / Donovan, Nerida J.

    Journal of virological methods. 2022 Jan., v. 299

    2022  

    Abstract: An apscaviroid, tentatively named citrus viroid VII (CVd-VII), was recently discovered in citrus in Australia. A diagnostic assay using real-time reverse transcription polymerase chain reaction was developed and validated to detect the viroid in citrus ... ...

    Abstract An apscaviroid, tentatively named citrus viroid VII (CVd-VII), was recently discovered in citrus in Australia. A diagnostic assay using real-time reverse transcription polymerase chain reaction was developed and validated to detect the viroid in citrus plants. The assay showed a high level of sensitivity, reliably detecting 2000 plasmid copies per reaction, while down to 20 plasmid copies per reaction were occasionally detected. The assay showed high specificity, producing no false positives or cross-reactivity with a range of other citrus graft-transmissible pathogens, including viroids, viruses and bacteria. The real-time assay was also found to be more sensitive than the available end-point reverse transcription polymerase chain reaction assay by a factor of 100,000 and could be a useful tool for the rapid detection of CVd-VII in diagnostic and research environments.
    Keywords Apscaviroid ; Citrus ; cross reaction ; plasmids ; rapid methods ; reverse transcriptase polymerase chain reaction ; viroids ; Australia
    Language English
    Dates of publication 2022-01
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 8013-5
    ISSN 1879-0984 ; 0166-0934
    ISSN (online) 1879-0984
    ISSN 0166-0934
    DOI 10.1016/j.jviromet.2021.114330
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  9. Article ; Online: Complete genome sequence of aucuba ringspot virus.

    Uke, Ayaka / Pinili, Marita S / Natsuaki, Keiko T / Geering, Andrew D W

    Archives of virology

    2021  Volume 166, Issue 4, Page(s) 1227–1230

    Abstract: A new badnavirus, aucuba ringspot virus (AuRV), was identified in plants of Aucuba japonica showing mild mosaic, vein banding, and yellow ringspot symptoms on the leaves. The complete nucleotide sequence of the AuRV genome was determined and found to be ... ...

    Abstract A new badnavirus, aucuba ringspot virus (AuRV), was identified in plants of Aucuba japonica showing mild mosaic, vein banding, and yellow ringspot symptoms on the leaves. The complete nucleotide sequence of the AuRV genome was determined and found to be 9,092 nt in length, and the virus was found to have a genome organization typical of members of the genus Badnavirus. ORF3 was predicted to encode a polyprotein containing conserved movement protein, coat protein, aspartic protease, reverse transcriptase (RT), and RNase H domains. Phylogenetic analysis suggested that this virus is most closely related to codonopsis vein clearing virus but belongs to a distinct species, based on only 69.6% nucleotide sequence identity within the part of ORF 3 encoding the RT and RNase H domains. The vector of AuRV is unknown, but based on phylogenetic relationships, it is predicted to be a type of aphid.
    MeSH term(s) Badnavirus/classification ; Badnavirus/genetics ; Badnavirus/isolation & purification ; Base Sequence ; DNA, Viral/genetics ; Genome, Viral/genetics ; Magnoliopsida/virology ; Open Reading Frames ; Phylogeny ; Plant Diseases/virology ; Plant Leaves/virology ; Polyproteins/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Viral Proteins/genetics
    Chemical Substances DNA, Viral ; Polyproteins ; Viral Proteins
    Language English
    Publishing date 2021-02-07
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-021-04977-4
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    Ud II Zs.110: Show issues Location:
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  10. Article: Detection of two poleroviruses infecting garlic (Allium sativum) in Australia

    Nurulita, Sari / Geering, Andrew D. W. / Crew, Kathleen S. / Harper, Stephen M. / Thomas, John E.

    Australasian plant pathology. 2022 July, v. 51, no. 4

    2022  

    Abstract: Two near complete polerovirus genomes were assembled using high throughput sequencing (HTS) data from two separate samples of garlic cultivar ‘Glenlarge’ grown in Gatton, Queensland, Australia. Whole genome sequence comparisons showed that one contig ... ...

    Abstract Two near complete polerovirus genomes were assembled using high throughput sequencing (HTS) data from two separate samples of garlic cultivar ‘Glenlarge’ grown in Gatton, Queensland, Australia. Whole genome sequence comparisons showed that one contig shared 96.7% nucleotide identity with phasey bean mild yellows virus (MT966032.1) and the other, 99.8% nucleotide identity with turnip yellows virus (MT586581.1). Phylogenetic analyses further revealed that the isolates fell within the PBMYV group 2 and TuYV group 2 clades, respectively. This is the first report of these poleroviruses infecting garlic.
    Keywords Allium sativum ; beans ; cultivars ; garlic ; genome ; nucleotide sequences ; phylogeny ; plant pathology ; turnips ; viruses ; Queensland
    Language English
    Dates of publication 2022-07
    Size p. 461-465.
    Publishing place Springer Netherlands
    Document type Article
    ZDB-ID 406733-2
    ISSN 1448-6032 ; 0815-3191
    ISSN (online) 1448-6032
    ISSN 0815-3191
    DOI 10.1007/s13313-022-00870-z
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