Aureusvirus

Abstract: A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31β algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed.

Abstract: Aureusvirus is a new genus of plant viruses typified by pothos latent virus (PoLV) and comprising cucumber leaf spot virus (CLSV), previously classified as definitive species in the genus Carmovirus. Aureusviruses are soil-borne viruses readily transmitted by sap inoculation to a moderate range of hosts. Natural transmissions of CLSV is by the chytrid fungus Olpidium bornovanus, whereas PoLV infects the host without the apparent intervention of a vector. Aureusviruses have isometric particles with size (c. 30 nm) and structure similar to those of the family Tombusviridae, to which the genus belongs. The genome consists of a molecule of single-stranded, positive-sense RNA c. 4.4 kb in size comprising five ORFs. The structural organization (i.e. number and order of genes) is virtually identical to that of members of the genus Tombusvirus. However, the aureusvirus genome has a smaller size and shows distinct differences in the amino acid sequence of some of the ORFs. ORF 1 encodes a 25 kDa product and terminates with a leaky amber codon the readthrough of which results in a 84 kDa protein (ORF 2) with the conserved motifs of RNA dependent RNA polymerase. ORF 3 encodes the coat protein (40-41 kDa), ORF 4 the movement protein (27 kDa), and ORF 5 a 14-17 kDa product responsible for symptom severity. Virions accumulate in great quantity in the cytoplasm, often forming crystalline aggregates, and in bubble-like evaginations of the tonoplast protruding into the vacuole. Replication is likely to occur in the cytoplasm with a stategy based on direct expression of the 5' proximal ORF and expression of downstream ORFs through subgenomic RNAs.

Abstract: A virus isolate from Pelargonium spp., provisionally designated UPEV (unknown pelargonium virus), had isometric particles 31-33 nm in diameter, with a granular surface structure similar to that of viruses in three genera of family Tombusviridae. Immunoelectron microscopy proved that UPEV was serologically distinct from all examined morphologically similar members of the family Tombusviridae. The induced cytopathology was characterized by large cytoplasmic virion aggregates and the formation of multivesicular bodies derived from mitochondria. Analysis of the complete ssRNA genome sequence revealed four open reading frames (ORFs) arranged like those of viruses in the genera Tombusvirus and Aureusvirus. Sequence comparisons indicated that three of the four ORFs had a high identity (52-97% identical amino acids) with the respective ORFs of tombusvirus species, especially with Carnation Italian ringspot virus, but not with those of viruses in other genera in Tombusviridae. On the contrary, UPEV coat protein had a low indentity (36-53% identical amino acids) with that of the aureusvirus Pothos latent virus. The data suggested that UPEV originated in a recombination event between a tombus- and an aureusvirus. According to its original host and symptom expression we proposed the new virus be named Pelargonium necrotic spot virus (PeNSV) and classified it as a distinct and new species in the genus Tombusvirus.

Abstract: Yam is a primary agricultural commodity in West African countries, especially Nigeria [http://faostat.fao.org]. Only a few viruses have been described to occur in yam (Dioscorea sp.) [1, 8]. These include Dioscorea bacilliform virus (genus Badnavirus) [3] and the potyviruses yam mosaic virus [2], yam mild mosaic virus [7] and yam chlorotic necrotic mosaic virus [22], which form bacilliform and filamentous virions, respectively. In 1998, a virus with isometric particles, referred to here as ‘‘yam spherical virus’’ (YSV), could be identified in a yam sample from Nigeria. In this paper, we report the complete genome sequence of YSV, a putative new member of the genus Aureusvirus. The genomes of viruses of the genus Aureusvirus (family Tombusviridae) consist of a single uncapped, nonpolyadenylated plus-strand RNA containing four open reading frames (ORFs). ORF1 codes for a highly conserved RNA-dependent RNA polymerase, and ORF2 codes for a coat protein (CP), which is expressed from a subgenomic (sg) RNA of approximately 2 kb. The protein encoded by ORF3 has been identified as a movement protein, and ORF4, nested in ORF3, codes for a silencing suppressor. ORFs 3 and 4 are translated from a second sgRNA (0.8 kb). Both sgRNAs are known to be encapsidated and also appear as dsRNA in infected plants [11]. Besides the type member pothos latent virus (PoLV) [16], only three other distinct members of the genus Aureusvirus (http://www. ictvonline.org/virusTaxonomy.asp?version=2012) have been completely sequenced: cucumber leaf spot virus (CLSV) [11], Johnsongrass chlorotic stripe mosaic virus [9] (JCSMV) and maize white line mosaic virus (MWLMV) [17]. Depending on the species, the RNA size ranges from 4.29 kb to 4.43 kb. The genome sequence of a fifth virus, sesame necrotic mosaic virus (SNMV), has been partially determined, and it also shows characteristics of and sequence identities to aureusvirus genomes [23]. Aureusviruses can be efficiently transmitted mechanically. Natural transmission occurs through soil (PoLV) [10, 18] or the soil-inhabiting fungus Olpidium bornovanus (CLSV) [4]. It has also been shown that CLSV can be efficiently transmitted in soil-less cucumber cultures by circulating irrigation water [15].