Nightshade curly top virus: A possible new virus of the genus Topocuvirus infecting Solanum nigrum in China

Virus-like symptoms, including leaf deformation and curling, were observed on nightshade (Solanum nigrum) in Zhejiang province, China. To identify possible pathogenic viruses or viroids, a symptomatic sample was subjected to deep sequencing of small interfering RNAs. Assembly of the resulting sequences led to identification of a novel geminivirus, provisionally designated nightshade curly top virus (NCTV). The complete genomic DNA sequence is 2,867 nucleotides that encodes seven open reading frames. NCTV shares 77.1 % overall nucleotide sequence identity, 86.3 % coat protein amino acid, and 78.9 % replication-associated protein amino acid sequence identity with Topocuvirus tomato pseudo-curly top virus (TPCTV). Polymerase chain reaction screening of nightshade field isolates indicated that NCTV is widely distributed in Zhejiang. Agrobacterium-mediated inoculation revealed that NCTV is highly infectious to Nicotiana benthamiana, Solanum nigrum, Solanum lycopersicum, and Solanum tuberosum. Based on pairwise comparisons and phylogenetic analyses, NCTV is proposed as a provisional member of the genus Topocuvirus.

A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing

The full-length genome of a novel Emaravirus has been identified and characterized from sycamore maple (Acer pseudoplatanus) - a tree species of significant importance in urban and forest areas - showing leaf mottle symptoms. RNA-Seq was performed using RNA preparations from a symptomatic and a symptomless maple tree. Purified double-stranded cDNA from each sample were used for RNA-Seq analysis on the Illumina HiSeq2500system and 14-198 MB data/sample of 100 bp-long paired-end sequence reads were generated. The sequence assembly and analysis revealed the presence of six RNA segments in the symptomatic sample (RNA1: 7,075 nt-long encoding the viral replicase; RNA2: 2,289 nt-long encoding the glycoprotein precursor; RNA3: 1,525 nt-long encoding the nucleocapsid protein; RNA4: 1,533 nt-long encoding the putative movement protein; RNA5: 1,825 nt-long encoding a hypothetical protein P5; RNA6: 1,179 nt-long encoding a hypothetical protein P6). Two independent HTS sequencing runs from the same symptomatic maple tree detected the same genome segments. For one of these sequencing runs the cDNA library was prepared using a primer targeting the conserved genome terminal region, known to be shared between emaraviruses genome segments and a high amount of sequence data was generated. We suggest, therefore, that the six identified genome segments represent the complete genome of a novel emaravirus from maple, which we tentatively name maple mottle-associated virus (MaMaV). RT-PCR assays were performed on symptomatic and non-symptomatic leaves of A. pseudoplatanus trees coming growing on two different locations in Berlin. MaMaV was only detected from symptomatic trees and all six RNAs were generally simultaneously detected. Non-symptomatic samples were consistently negative for MaMaV. These results suggest that MaMaV might be the symptom inducing virus in the sampled trees. In the present state of the art, this is the first time an Emaravirus is described from maple and is fully genetically characterized.

Illumina Sequencing Reveals the First Near-Complete Genome Sequence of Ugandan Passiflora Virus

Here, we present the first near-complete genome of Ugandan Passiflora virus (UPV) sequenced from a symptomatic sample of KH7 passion fruit (Passiflora edulis Sims) variety. UPV had limited amino acid identity with other potyviruses known to cause passion fruit woodiness disease (PWD).

First Report of Calibrachoa mottle virus Infecting Petunia

Calibrachoa mottle virus (CbMV), a tentative carmovirus, was first isolated and reported by Liu et al. (1) from infected Calibrachoa plants. During the spring of 2003, petunia samples from Florida and California sent to testing services at Agdia, Inc (Elkhart IN) tested positive for CbMV by enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay (ImmunoStrips). These samples also tested positive by carmovirus group-specific polymerase chain reaction (PCR) primers and by immunocapture PCR (2). RNA extracted from these samples with the RNeasy Plant Kit (Qiagen Inc., Valencia, CA) hybridized with a digoxigenin labeled probe derived from purified CbMV viral RNA. All plant samples that tested positive for CbMV were symptomless except one symptomatic sample that also tested positive for Tobacco mosaic virus. From samples that tested positive for CbMV only, mechanical inoculations were made to Chenopodium quinoa at a USDA-ARS greenhouse in Salinas, CA. Representative single, local lesions were used to inoculate additional C. quinoa plants. The resulting local lesions from these inoculations were freeze-dried and further used as virus inoculum (CbMV petunia). Similar inoculum was made with CbMV isolated from Calibrachoa plants (CbMV calibrachoa). Virus-free Petunia hybrida cultivars Surfinia ‘Baby Pink’ and Surfinia ‘Violet’ (Jackson and Perkins Inc., Somis, CA) were mechanically inoculated with CbMV petunia and CbMV calibrachoa. Four weeks postinoculation, all plants were tested using ELISA for the presence of CbMV. In greenhouse conditions, 14.3% of ‘Baby Pink’ plants were positive for CbMV petunia, whereas none were positive for CbMV calibrachoa. ‘Violet’ plants were 64.3 and 33.3% positive for CbMV petunia and CbMV calibrachoa, respectively. None of the positive plants expressed virus-like symptoms. Virus particles resembling those of CbMV were observed from infected petunia plants with transmission electron microscopy in leaf-dip preparations. To our knowledge, this is the first report of CbMV infecting petunia. Commercial reproduction of petunia plants and maintenance of genetic mother stock are usually by vegetative propagation. CbMV can be transmitted mechanically and is readily propagated along with its host. To produce healthy petunia plants, virus-free mother stock should be used, which requires regular screening of mother stock for CbMV. Reference: (1) H.-Y. Liu et al. Plant Dis. 87:167, 2003. (2) A. M. Harness et al. (Abstr.) Phytopathology 92:S34, 2002.