Nanopore sequencing of tomato mottle leaf distortion virus, a new bipartite begomovirus infecting tomato in Brazil

During a survey in a tomato field in Luziânia (Goiás State, Brazil), a plant showing mottling, chlorotic spots, and leaf distortion was found. A new bipartite begomovirus was found by Nanopore sequencing, and the full DNA-A sequence was confirmed by Sanger sequencing. The highest nucleotide identity match of this DNA-A genome (2596 bases) was 81.65% with tomato golden leaf deformation virus (HM357456). Due to the current species demarcation criterion of 91% of nucleotide identity (DNA-A), we propose it as a new member of the genus Begomovirus, named Tomato mottle leaf distortion virus.

A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris)

We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.

Identification and Genetic Characterization of a Novel Respirovirus in Alpine Chamois (Rupicapra rupicapra rupicapra)

The Respirovirus genus, family Paramamixoviridae, includes respiratory viral pathogens. Here we report the identification and genetic characterization of a respirovirus in an Alpine chamois showing interstitial pneumonia associated with catarrhal bronchopneumonia. The full-genome characterization of this respirovirus, named ChamoisRV/IT2014, revealed low similarities to caprine respirovirus (77.1%), bovine respirovirus (74.5%) and human respirovirus (72.0%). The phylogenetic analyses based on the full-length genome sequence of the novel isolate and reference respirovirus strains showed that ChamoisRV/IT2014 clustered with caprine respirovirus but formed a separate branch. The phylogenetic tree topology of complete large protein amino acid sequences, representing the current species demarcation criterion for Respirovirus genus, showed a 0.05 branch length of ChamoisRV/IT2014 sequence between the nearest node and the tip of the branch, suggesting that this virus belongs to a novel species. This new isolate in a new host species raises several questions to be addressed on the epidemiological role of chamois and the risks of cross-transmission between wild ruminants and livestock.

Partial molecular characterization of begomoviruses isolated from weeds collected in tomato crops in the southeast of Valle del Cauca, Colombia

Weeds are usually considered as a source of new viruses but are often neglected during diversity studies. Previously eleven samples of weeds were collected along the edges of a tomato crop field located in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the Southeast of Valle del Cauca. These samples were positive for begomoviruses but their molecular characterization had not been done until now. For each sample, DNA fragments were cloned, sequenced and analyzed. Nucleotide sequence analysis of viral fragments showed the presence of six different begomoviruses: two virus isolated from Lantana camara, Desmodium sp. and Amaranthus dubius were previously described as potato yellow mosaic virus (PYMV) and passionfruit leaf distortion virus (PLDV), respectively; other four virus which were isolated from L. camara, A. dubius, Rivina humilis, Desmodium sp., Rhynchosia minima, Hybanthus attenuatus, Verbena sp., Croton hirtus and Caesalpinia sp., showed its highest nucleotide sequence identity (89%) with bean chlorotic mosaic virus (BChMV), datura leaf distortion virus (DaLDV) and rhynchosia golden mosaic Yucatan virus (RhGMYV). Cloned viruses fragments from these weeds could be new begomoviruses not previously reported before, this in accordance with the ICTV species demarcation criterion for the genus Begomovirus (≥91 % sequence identity). Mixed infections of begomoviruses in Desmodium sp. and A. dubius weeds also was found in this analysis. Finally, this paper reports by the first time to three alternative begomoviruses weeds hosts that infect tomato and passion fruit crops: A. dubius for PYMV, and L. camara and Desmodium sp. for PLDV, respectively.