[Show abstract][Hide abstract] ABSTRACT: Cucumber Bulgarian latent virus (CBLV) was first reported from cucumber in Bulgaria in 2003 and has been assigned to the genus Tombusvirus. Ten years after the first and only report of CBLV, an isolate from a cucumber sample collected in Iran was characterized. Its complete genomic sequence was determined and analysed. Except for the coat protein, CBLV shows the highest sequence identities to the isolates of other species of the genus Tombusvirus. However, sequence comparison and phylogenetic analyses based on the coat protein (CP) revealed that CBLV is more closely related to the genus Aureusvirus rather than to the isolates of the genus Tombusvirus. The sequence identities to some aureusviruses are above the species demarcation threshold value, demonstrating that CBLV is an unusual tombusvirus species. This suggests that it is necessary to review the CP threshold value for species demarcation in the genus Aureusvirus. In addition, CBLV has an intermediate genome size compared to other tombus- and aureusviruses. Several polyclonal antisera raised against different tombus- and aureusviruses were used to assess the serological relation to CBLV. The ELISA results indicate that CBLV is not serologically related to any of those tested.
Journal of Phytopathology 11/2014; · 1.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Etiological studies of a recently emerged bushy top disease of tobacco in Ethiopia indicated that a ~4.5-kb dsRNA from infected plants represents an umbravirus, whereas a smaller band (~0.5 kb) is that of a new satellite RNA. Potato leafroll virus was also consistently associated with the disease. The three agents, whose experimental host ranges are restricted to members of the family Solanaceae, always occurred together in field samples and are transmitted together by the aphid Myzus persicae nicotianae. The umbravirus, which represents a new species, is most closely related to groundnut rosette virus, and the name Ethiopian tobacco bushy top virus is proposed.
[Show abstract][Hide abstract] ABSTRACT: During surveys conducted in 2012–2013, viruslike symptoms of chlorotic
spots with, in some cases, a necrotic centre in older leaves were observed
in field- and greenhouse-grown cucumber (Cucumis sativus L.), melon
(C. melo L.) and squash (Cucurbita sp.) in the major cucurbit cultivation
regions in Iran. Leaf samples were collected and tested for the presence of
Cucumber leaf spot virus (CLSV, genus Aureusvirus, family Tombusviridae) by
a virus specific double-antibody sandwich enzyme-linked immunosorbent
assay (DAS-ELISA). CLSV was detected in four of eight surveyed
provinces in melon, cucumber and squash. When plant sap of ELISA
positive samples was used to mechanically inoculate healthy squash
plants, chlorotic spots with, in some cases, necrotic centres were observed
on the inoculated leaves 20–25 days postinoculation. The presence of
CLSV was confirmed by reverse transcription polymerase chain reactions
using specific primers amplifying the entire coat protein gene of CLSV.
Sequence comparison with sequences available at GenBank showed 93%
nucleotide sequence identity to CLSV isolates from Israel (DQ227315)
and Canada (EU127904), the only CLSV coat protein sequences available.
To our knowledge, this is the first report of the occurrence of CLSV in
Journal of Phytopathology 01/2014; 162:205-208. · 1.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Despite the seemingly continuous development of newer and ever more elaborate methods for detecting and identifying viruses, very few of these new methods get adopted for routine use in testing laboratories, often despite the many and varied claimed advantages they possess. To understand why the rate of uptake of new technologies is so low, requires a strong understanding of what makes a good routine diagnostic tool to begin. This can be done by looking at the two most successfully established plant virus detection methods: enzyme-linked immunosorbant assay (ELISA) and more recently introduced real-time polymerase chain reaction (PCR). By examining the characteristics of this pair of technologies, it becomes clear that they share many benefits, such as an industry standard format and high levels of repeatability and reproducibility. These combine to make methods that are accessible to testing labs, which are easy to establish and robust in their use, even with new and inexperienced users. Hence, to ensure the establishment of new techniques it is necessary to not only provide benefits not found with ELISA or real-time PCR, but also to provide a platform that is easy to establish and use. In plant virus diagnostics, recent developments can be clustered into three core areas: 1. techniques that can be performed in the field or resource poor locations (e.g., loop-mediated isothermal amplification LAMP); 2. multiplex methods that are able to detect many viruses in a single test (e.g., Luminex bead arrays); and 3. methods suited to virus discovery (e.g., next generation sequencing, NGS). Field based methods are not new, with Lateral Flow Devices (LFDs) for the detection being available for a number of years now. However the widespread uptake of this technology remains poor. LAMP does offer significant advantages over LFDs, in terms of sensitivity and generic application, but still faces challenges in terms of establishment. It is likely that the main barrier to the uptake of field-based technologies is behavioral influences, rather than specific concerns about the performance of the technologies themselves. To overcome this, a new relationship will need to develop between centralized testing laboratories offering services and those requiring tests; a relationship which is currently in its infancy. Looking further into the future, virus discovery and multiplex methods seem to converge as NGS becomes ever cheaper, easier to perform and can provide high levels of multiplexing without the use of virus specific reagents. So ultimately the key challenge from a routine testing lab perspective will not be one of investment in platforms-which could even be outsourced to commercial sequencing services-but one of having the skills and expertise to analyse the large datasets generated and their subsequent interpretation. In conclusion, only time will tell which of the next-generation of methods currently in development will become the routine diagnostics of the future. This will be determined through a combination of factors. And while the technology itself will have to offer performance advantages over existing methods in order to supplant them, it is likely to be human factors e.g., the behaviors of end users, laboratories and policy makers, the availability of appropriate expertise, that ultimately determine which ones become established. Hence factors cannot be ignored and early engagement with diagnostic stakeholders is essential.
[Show abstract][Hide abstract] ABSTRACT: The availability of characterised reference isolates of plant pathogens is of crucial importance for research and diagnostic laboratories. The Q-bank Plant Viruses and Viroids database contains data and information on plant viruses and viroids, with the unique feature that it is linked to specimens present in publicly available physical collections. The Q-bank database aims to share data and information on the virus and viroid species and their availability between research and diagnostic laboratories. Currently the database focuses on regulated virus species. In future more plant viruses and viroids will be included to provide a comprehensive data and information system. The curators invite virologists worldwide to participate in this international initiative by making their data and isolates available via Q-bank (http://www.q-bank.eu). La base de données et les collections Virus et Viroïdes des Plantes de Q-bank La disponibilité d'isolats de référence caractérisés est d'une importance cruciale pour les laboratoires de recherche et de diagnostic. La base de données de Q-bank sur les Virus et Viroïdes des plantes contient des données et des informations sur les virus et viroïdes, avec l'avantage d’être liée à des spécimens présents dans des collections physiques qui sont disponibles publiquement. La base de données Q-bank vise à permettre le partage de données et d'informations sur les espèces de virus et de viroïdes et leur mise à disposition entre laboratoires de recherche et de diagnostic. Actuellement, la base de données se concentre sur les espèces de virus réglementées. A l'avenir, d'autres virus et viroïdes des végétaux seront ajoutés pour fournir un système de données et d'informations cohérent et complet. Les curateurs invitent les virologistes dans le monde entier à participer à cette initiative internationale en rendant leurs données et leurs isolats disponibles au travers de Q-bank (http://www.q-bank.eu). Бaзa дaнныч о вирусaч и вироидaч рaстений и коллекции Q-bank Для иccлeдoвaтeльcкиx и диaгнocтичecкиx лaбopaтopий дocтyпнocть oxapaктepизoвaнныx cпpaвoчныx изoлятoв пaтoгeнoв pacтeний имeeт пepвocтeпeннoe знaчeниe. Бaзa дaнныx пoд нaзвaниeм «The Q-bank Plant Viruses & Viroids» coдepжит дaнныe и инфopмaцию o виpycax и виpoидax pacтeний и имeeт тy yникaльнyю ocoбeннocть, чтo oнa cвязaнa c экзeмпляpaми, нaличecтвyющими в пyбличнo дocтyпныx кoллeкцияx. Бaзa дaнныx Q-bank cтaвит cвoeй цeлью oбмeн дaнными и инфopмaциeй o видax виpycoв и виpoидax и иx дocтyпнocти для иccлeдoвaтeльcкиx и диaгнocтичecкиx лaбopaтopий. B нacтoящee вpeмя бaзa дaнныx cocpeдoтoчeнa нa peгyлиpyeмыx видax виpycoв. B бyдyщeм в нee бyдeт включeнo бoльшee кoличecтвo виpycoв и виpoидoв pacтeний, c тeм чтoбы oбecпeчивaлacь пoлнoтa дaнныx и инфopмaциoнныx cиcтeм. Кypaтopы этoй бaзы пpeдлaгaют виpoлoгaм вceгo миpa пoyчacтвoвaть в этoй мeждyнapoднoй инициaтивe пyтeм пpeдocтaвлeния cвoиx дaнныx и изoлятoв чepeз Q-bank (<http://www.q-bank.eu>).
[Show abstract][Hide abstract] ABSTRACT: The complete genome of a tomato mild mottle virus (ToMMV) isolate was analysed, and some biological features were characterized. The ssRNA genome of ToMMV from Ethiopia encompasses 9283 nucleotides (excluding the 3' poly(A) tail) and encodes a polyprotein of 3011 amino acids. Phylogenetic and pairwise comparisons with other members of the family Potyviridae revealed that ToMMV is the most divergent member of the genus Ipomovirus, with a genome organization similar to that of members of the species Sweet potato mild mottle virus, the type species of the genus. In contrast to earlier reports, ToMMV isolates from Yemen and Ethiopia were not transmitted by the aphid Myzus persicae, but they were transmitted very erratically by the whitefly Bemisia tabaci. A comparison of the 3'-proximal sequences of different isolates provided evidence for geographically associated genetic variation.
Archives of Virology 11/2011; 157(2):353-7. · 2.28 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In 1993, a virus causing red mosaic and leaf distortion has been isolated from black bryony (Tamus communis) in Italy. Based on particle properties and serology, the virus was assigned to the genus Potexvirus and named Tamus red mosaic virus (TRMV), pending a genome sequence. The original Italian TRMV isolate was submitted to the DSMZ plant virus collection (PV-0397). To confirm the taxonomic status of the virus, the entire genome sequence was determined comprising 6,495 nucleotides excluding the poly(A)-tail. Five putative open reading frames (ORFs) in an arrangement typical for potexviruses were predicted. TRMV is closely related to but distinct from Clover yellow mosaic virus and Allium virus X. In addition to previous morphological and serological characterization, the results presented in this study further reinforce the classification of TRMV as a distinct virus species of the genus Potexvirus.
[Show abstract][Hide abstract] ABSTRACT: In vegetatively propagated Alstroemeria plants that showed pronounced stunting and necrotic leaf spots, a tobravirus infection was diagnosed in which one tobacco rattle virus (TRV, strain AL) RNA1 species was associated with seven different RNA2 species. The latter differed considerably in size and in the types of their 3' RNA1-related sequences. The 5' RNA2-specific part of all these RNA2 molecules showed almost 100% sequence identity with that of RNA2 of the TRV isolate TCM from tulip, but in some of these RNA2 molecules it was shorter than in the TCM isolate, whereas in others it was longer. One of the TRV AL RNA2 molecules, i.e. TC3'PE-a, contained the full set of three full-length RNA2-specific ORFs (ORF2a, -2b and -2c), whereas the previously analysed TCM sequence contained only ORF2a and -2b. In four of these TRV AL RNA2 molecules, i.e. those that had a relatively short RNA2-specific part, the 3' end was identical to that of the cognate TRV AL RNA1, but in the other three, which had a long RNA2-specific part, it was closely related to that of pea early browning virus (PEBV) RNA1, which was not detected in the infected plants. A comparison with previously described TRV/PEBV RNA2 recombinants suggested that the various TRV AL RNA2 molecules may represent various steps and side steps in an evolutionary process, which is apt to open the wide host range of TRV also to PEBV-derived RNA2 species.
Journal of General Virology 12/2010; 92(Pt 4):988-96. · 3.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cassava brown streak virus (CBSV) isolates were analysed from symptomatic cassava collected between 1997 and 2008 in the major cultivation regions of East Africa. An analysis of complete RNA genomes of seven isolates from Kenya, Tanzania, Mozambique, Uganda and Malawi revealed a common genome structure, but the isolates clearly clustered in two distinct clades. The first comprised isolates from Kenya, Uganda, Malawi, north-western Tanzania and the CBSV described previously, and shared between 87 and 95% nucleotide sequence identity, whilst the second included isolates from coastal regions of Mozambique and Tanzania, which shared only 70% nucleotide sequence identities with isolates of the first clade. When the amino acid sequences of viral proteins were compared, identities as low as 47% (Ham1) and 59% (P1) between the two clades were found. An antiserum obtained against the capsid protein of a clade 1 isolate identified a 43 kDa protein in clade 1 isolates and a 45 kDa protein in clade 2 isolates. Several cassava cultivars were susceptible to isolates of clade 2 but resistant to those of clade 1. The differences observed both in biological behaviour and in genomic and protein sequences indicate that cassava brown streak disease in East Africa is caused by at least two distinct virus species. It is suggested that those of clade 1 retain the species name Cassava brown streak virus, whilst those of clade 2 be classified as Cassava brown streak Mozambique virus.
Journal of General Virology 05/2010; 91(Pt 5):1365-72. · 3.13 Impact Factor