Expanding the repertoire of the plant-infecting ophioviruses through metatranscriptomics data

Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with nonenveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus.Instituto de Biotecnología y Biología Molecula

Viromes of Ten Alfalfa Plants in Australia Reveal Diverse Known Viruses and a Novel RNA Virus

Alfalfa plants in the field can display a range of virus-like symptoms, especially when grown over many years for seed production. Most known alfalfa viruses have RNA genomes, some of which can be detected using diagnostic assays, but many viruses of alfalfa are not well characterized. This study aims to identify the RNA and DNA virus complexes associated with alfalfa plants in Australia. To maximize the detection of RNA viruses, we purified double-stranded RNA (dsRNA) for high throughput sequencing and characterized the viromes of ten alfalfa samples that showed diverse virus-like symptoms. Using Illumina sequencing of tagged cDNA libraries from immune-captured dsRNA, we identified sequences of the single-stranded RNA viruses, alfalfa mosaic virus (AMV), bean leafroll virus, a new emaravirus tentatively named alfalfa ringspot-associated virus, and persistent dsRNA viruses belonging to the families Amalgaviridae and Partitiviridae. Furthermore, rolling circle amplification and restriction enzyme digestion revealed the complete genome of chickpea chlorosis Australia virus, a mastrevirus (family Geminiviridae) previously reported only from chickpea and French bean that was 97% identical to the chickpea isolate. The sequence data also enabled the assembly of the first complete genome (RNAs 1–3) of an Australian AMV isolate from alfalfa

The westward journey of alfalfa leaf curl virus

Alfalfa leaf curl virus (ALCV), which causes severe disease symptoms in alfalfa (Medicago sativa L.) and is transmitted by the widespread aphid species, Aphis craccivora Koch, has been found throughout the Mediterranean basin as well as in Iran and Argentina. Here we reconstruct the evolutionary history of ALCV and attempt to determine whether the recent discovery and widespread detection of ALCV is attributable either to past diagnostic biases or to the emergence and global spread of the virus over the past few years. One hundred and twenty ALCV complete genome sequences recovered from ten countries were analyzed and four ALCV genotypes (ALCV-A, ALCV-B, ALCV-C, and ALCV-D) were clearly distinguished. We further confirm that ALCV isolates are highly recombinogenic and that recombination has been a major determinant in the origins of the various genotypes. Collectively, the sequence data support the hypothesis that, of all the analyzed locations, ALCV likely emerged and diversified in the Middle East before spreading to the western Mediterranean basin and Argentina

Taxonomy of the order Mononegavirales : update 2016

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV)

Taxonomy of the order Mononegavirales: update 2017.

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV)

Letter to the Editor: bean-associated cytorhabdovirus and papaya cytorhabdovirus are strains of the same virus

Recently, Alves-Freitas and colleagues [...]

First Report of Orchid Fleck Virus in Lilyturf (Liriope spicata) in Australia

Liriope spicata (Asparagaceae) is an evergreen ornamental plant commonly referred to as lilyturf, creeping liriope, monkey grass, or creeping lilyturf, and is widely grown as groundcover and for erosion control (Fantz 2008). In April 2015, lilyturf plants with bright yellow flecks on the leaves were observed in landscape plantings across the St. Lucia campus of the University of Queensland, Brisbane, Australia. These symptoms were reminiscent of those observed on leaves of orchid species infected by Orchid fleck virus (OFV) (Kubo et al. 2009). Symptomatic leaf samples were collected and analyzed in a JEM-1400 transmission electron microscope (JEOL Ltd., Tokyo, Japan). Leaf dips were prepared by breaking up symptomatic tissue in 1% ammonium molybdate, pH 7.0 negative stain and extracts were placed on nitrocellulose-coated copper grids. Digital micrographs were captured with an Orius digital camera (Gatan Inc., Pleasanton, CA). Typical nonenveloped, rhabdovirus-like, bacilliform particles measuring ∼45 × 95 nm were observed, similar to those of OFV from infected orchids (Kondo et al. 2006). Total RNA was extracted from symptomatic tissue using an RNeasy Plant Mini Kit (Qiagen) and subjected to RT-PCR using the Superscript III One Step RT-PCR System with Platinum Taq DNA Polymerase (Thermo Fisher) and OFV nucleoprotein (N) gene primers polydT/SP6 (5′-GATTTAGGTGACACTATAGTTTTTTTTTTTTTTTTT(A/G/C)-3′) and mN2 (5′-TGCAGGAATATAGCCGACATGTT-3′) (Blanchfield et al. 2001). Agarose gel electrophoresis showed a single amplicon of ∼800 bp, comparable to the OFV positive control. DNA from both the lilyturf (DAF Plant Virus Collection Accession No. 5216) and a cymbidium OFV control (Accession No. 703) amplicons were gel-purified and cloned into pGEM-T Easy vector (Promega, Madison, WI) and sequenced using dideoxynucleotide sequencing at the Australian Genome Research Facility (Brisbane, Australia). A GenBank BLASTx search of the lilyturf virus N gene sequence of 658 nt showed 100% match to the N protein sequence of an Australian OFV isolate (Genbank Accession No. AAK09392 and e-value 1e-143). The partial N gene nucleotide sequence of the lilyturf OFV isolate #5216 was 99% identical to the cymbidium OFV isolate. Both sequences have been deposited in GenBank with Accession Nos. KT947974 and KT947975, respectively. Based on the observed symptoms, particle morphology, N gene amplicon using OFV primers, and high sequence identity with other OFV sequences, we conclude that the lilyturf plants were infected with OFV. This is the first report of OFV infecting L. spicata. This alternative host may play a possible role in OFV spread to orchids or other ornamental species that are colonized by its Brevipalpus sp. mite vector

Analysis of the coding-complete genomic sequence of groundnut ringspot virus suggests a common ancestor with tomato chlorotic spot virus

[EN] Groundnut ringspot virus (GRSV) and tomato chlorotic spot virus (TCSV) share biological and serological properties, so their identification is carried out by molecular methods. Their genomes consist of three segmented RNAs: L, M and S. The finding of a reassortant between these two viruses may complicate correct virus identification and requires the characterization of the complete genome. Therefore, we present for the first time the complete sequences of all the genes encoded by a GRSV isolate. The high level of sequence similarity between GRSV and TCSV (over 90 % identity) observed in the genes and proteins encoded in the M RNA support previous results indicating that these viruses probably have a common ancestor.This work was supported by Fundacion Mani Argentino and the PNIND PE 1108072 project of Instituto Nacional de Tecnologia Agropecuaria (INTA).De Breuil, S.; Cañizares Sales, J.; Blanca Postigo, JM.; Bejerman, N.; Trucco, V.; Giolitti, F.; Ziarsolo Areitioaurtena, P.... 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