Two Complete Genome Sequences of Phasey Bean Mild Yellows Virus, a Novel Member of the
            <i>Luteoviridae</i>
            from Australia

Sharman, Murray; Kehoe, Monica A.; Coutts, B. A.; Leur, Joop van; Filardo, Fiona; Thomas, J. E.

doi:10.1128/genomea.01569-15

Cited by 14 publications

(6 citation statements)

References 8 publications

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“…It is nevertheless likely that this luteovirus-like sequence is from a virus that should be classified as belonging to the Polerovirus genus of the Luteoviridae . It is also noteworthy that ORF2 shares >80% nucleotide sequence identity with that of PBMYV, a novel polerovirus also isolated from phasey bean ( Macroptilium lathyroides ), a legume of the Fabaceae family [ 43 ]. However, ORF3 and ORF4 share <80% nucleotidic identity with the corresponding ORFs of PBMYV, suggests that the new virus could potentially be considered as either a new variant of PBMYV or a new Polerovirus species.…”

Section: Resultsmentioning

confidence: 99%

Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso

et al. 2016

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Cowpea, (Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as “poor man’s meat”, cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. However, African cowpea production can be seriously constrained by viral diseases that reduce yields. While twelve cowpea-infecting viruses have been reported from Africa, only three of these have so-far been reported from Burkina Faso. Here we use a virion-associated nucleic acids (VANA)-based metagenomics method to screen for the presence of cowpea viruses from plants collected from the three agro-climatic zones of Burkina Faso. Besides the three cowpea-infecting virus species which have previously been reported from Burkina Faso (Cowpea aphid borne mosaic virus [Family Potyviridae], the Blackeye cowpea mosaic virus—a strain of Bean common mosaic virus—[Family Potyviridae] and Cowpea mottle virus [Family Tombusviridae]) five additional viruses were identified: Southern cowpea mosaic virus (Sobemovirus genus), two previously uncharacterised polerovirus-like species (Family Luteoviridae), a previously uncharacterised tombusvirus-like species (Family Tombusviridae) and a previously uncharacterised mycotymovirus-like species (Family Tymoviridae). Overall, potyviruses were the most prevalent cowpea viruses (detected in 65.5% of samples) and the Southern Sudan zone of Burkina Faso was found to harbour the greatest degrees of viral diversity and viral prevalence. Partial genome sequences of the two novel polerovirus-like and tombusvirus-like species were determined and RT-PCR primers were designed for use in Burkina Faso to routinely detect all of these cowpea-associated viruses.

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Section: Resultsmentioning

confidence: 99%

Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso

et al. 2016

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“…The number of novel viruses discovered needed for a high-profile paper has increased by logarithms (Krishnamurthy et al, 2016;Shi et al, 2016). In the absence of particular phenotypic data or wet-lab viral characterization, many authors have turned to Genome Announcements, biorxiv, or simply uploading to Genbank with extra metadata, figuring that sequencing is the most likely future method of both detection and discovery (Debat, 2017;Greninger and DeRisi, 2015e,f;Karamendin et al, 2016;Sharman et al, 2016;Sparks et al, 2013). Given the glut of new viruses, expansion of sequencing, and the time it takes to publish, scientists may be more likely to align to your novel virus rather than read about it in a journal and decide to screen for it.…”

Section: Experimenting With Functionmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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“…In 1993, Horn et al first identified CpCDV, a virus of the family Geminiviridae, in India [ 25 ], and 19 types of CpCDV (CpCDV-a to s strains) have been reported. Then, CpCDV viruses have also been identified in the Middle East, Africa, South Africa, North Africa, South Asia, and the Arabian Peninsula [ 13 , 18 , 26 – 28 , 36 – 41 ]. Three CpCDV species of chickpea chlorotic dwarf Sudan virus (CCDSV), chickpea chlorotic dwarf Pakistan virus (CCDPV), and chickpea chlorotic dwarf Syria virus (CCDSV) can infest chickpea [ 6 ].…”

Section: Virus Characteristics Of Chickpeamentioning

confidence: 99%

Identification of New Chickpea Virus and Control of Chickpea Virus Disease

Cun

2022

Evidence-Based Complementary and Alternative Medicine

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Objective. The objective of the study was to discuss the classification, virus characteristics, detection methods, and control measures of chickpea virus, with an aim to provide a theoretical basis for identification of new chickpea virus and control of chickpea virus disease. Methods. The domestic and foreign studies were reviewed, and the virus coat protein or nucleic acid sequence was identified by immunological and molecular diagnostic techniques. Results. There were 14 main types of chickpea viruses attacking, and seven Luteoviridae viruses were reported, namely, chickpea chlorotic stunt virus (CpCSV), bean leafroll virus (BLRV), beet western yellows virus (BWYV), soybean dwarf virus (SbDV), cotton leafroll dwarf virus (CLRDV), cucurbit aphid-borne yellows virus (CABYV), and phasey bean mild yellows virus (PhBMYV). The family Geminiviridae includes chickpea chlorotic dwarf virus (CpCDV), chickpea chlorosis virus (CpCV), chickpea redleaf virus (CpRLV), chickpea yellows virus (CpYV), and mastrevirus. The family Nanoviridae is dominated by the faba bean necrotic yellows virus (FBNYV). The family Bromoviridae includes cucumber mosaic virus (CMV) and alfalfa mosaic virus (AMV). Conclusion. At present, there are mainly 12 types of viruses infecting chickpeas, which are transmitted by leafhoppers or aphids and are associated with symptoms such as yellowing, chlorosis, and stunted pod development, resulting in serious yield loss. Correct use of various molecular diagnostic tools to detect and identify chickpea virus can accurately assess chickpea virus infection and provide a basis for the prevention and treatment of chickpea virus disease.

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Two Complete Genome Sequences of Phasey Bean Mild Yellows Virus, a Novel Member of the Luteoviridae from Australia

Cited by 14 publications

References 8 publications

Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso

Metagenomic-Based Screening and Molecular Characterization of Cowpea-Infecting Viruses in Burkina Faso

A decade of RNA virus metagenomics is (not) enough

Identification of New Chickpea Virus and Control of Chickpea Virus Disease

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