A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus tolerance Ty-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n = 107) were field-collected, circular DNA-enriched, subdivided into pools (with and without Ty-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without the Ty-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novel Begomovirus species were identified exclusively in samples without the Ty-1 gene. A novel begomovirus was found only in the Ty-1 pool, being the only species associated with severe symptoms in Ty-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation to Ty-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.

Severe yield losses induced by a complex of whitefly–transmitted Begomovirus species (family Geminiviridae) have been reported in tomatoes in Brazil (Reis et al. 2020). Nine isolates were obtained from tomato plants exhibiting begomovirus–like symptoms (viz. apical and interveinal chlorosis, yellow spots, and stunting) during independent field surveys: one isolate in Sumaré, São Paulo–SP State (isolate SP–066) in 2001, two in Serra Negra, Minas Gerais–MG (MG–012 and MG–016) in 2002, five in Caxias do Sul, Rio Grande do Sul–RS (RS–039, RS–045, RS–046, RS–047 and RS–058) in 2011 and one in Domingos Martins, Espírito Santo–ES (ES–148) in 2016. Disease incidence across all sampled fields ranged from 30% (in Domingos Martins–ES) to 90% in Sumaré–SP. Total DNA extraction was done by a modified CTAB method (Boiteux et al., 1999). Begomovirus infection was confirmed in all isolates by selective amplification of viral DNA–A segments using the primer pairs ‘PAL1v1978 / PAR1c496’ (Rojas et al., 1993) and ‘BegomoAFor1’ / ‘BegomoARev1’ (Ha et al., 2006), which produce two large and non–overlapping segments (≈1120 bp and ≈1205 bp, respectively). These PCR amplicons were initially characterized via direct Sanger dideoxy sequencing at CNPH. BLASTn analysis of the partial DNA–A genomes of these nine isolates indicated identity levels of 95–97% to three euphorbia yellow mosaic virus (EuYMV) reference isolates (= KY559532, JF756674, and KY559583) found infecting the weed Euphorbia heterophylla L. The entire DNA–A (2,609 nts = MN746971) and DNA–B (2,579 nts = MN746970) components of the MG–016 isolate were obtained via high–performance sequencing using Illumina HiSeq 2500 system (Macrogen Inc., South Korea). Sequences were assembled with the CLC Genomics Workbench program 10. Contigs were validated by BLASTx and BLASTn and compared to the ssDNA virus database at NCBI (www.ncbi.nlm.nih.gov). The fully–characterized MG–016 isolate displayed identity levels ranging from 97 to 99% to the EuYMV reference isolates as well as similar genomic features such as the conserved TATA box, nonanucleotide, and iterons (that were in agreement with a cognate nature of the DNA–A and DNA–B components). A partial sequence of the DNA–B genome was also obtained for the MG–012 isolate (MT7831942). The isolates MG–012 and MG–016 were found in mixed infections with tomato severe rugose virus (ToSRV) and tomato golden vein virus (TGVV), respectively. In addition, the complete DNA–A genomes of ES–148 (MN746972) and SP–066 (MN782438) were also obtained via a combination of primer walking and Sanger dideoxy sequencing, displaying 96–98% identity to EuYMV isolates. To our knowledge, this is the first report of multiple and independent events of natural infection of tomatoes by EuYMV isolates. Our results confirm the natural host status of tomatoes to EuYMV isolates as indicated in previous infectivity assays using biolistic inoculation (Barreto et al., 2013). The weed E. heterophylla is widely disseminated and very often present within tomato fields due to its higher levels of tolerance to the major herbicide (metribuzin) employed in this crop. Therefore, this weed may act as a persistent reservoir of tomato–infecting EuYMV isolates, which may allow the selection of viral populations potentially more adapted to this vegetable crop.

An increased incidence and severity of Orthotospovirus species has been observed in the peanut crop. The typical symptoms of the virus, usually known as ringspot in peanut and spotted wilt in other crops, include mosaic, chlorotic ring-shaped spots, necrosis, and plant stunting. This study aimed to verify the occurrence of this virus in peanut growing areas in the São Paulo State, Brazil, identify the predominant virus species, and determine losses resulting from the presence of this virus. Surveys were carried out in four peanut commercial areas sown in the municipalities of Santa Adélia and Cândido Rodrigues in the 2014/2015 season using the cultivar Granoleico. The following parameters were evaluated: plant stand, number of plants with symptoms, and severity of these symptoms through a scoring scale of visual symptoms. The results showed that the predominant virus species is Groundnut ringspot tospovirus (GRSV). Also, the lower the stand is, the higher the percentage of plants with virus symptoms. The mean incidence of GRSV in commercial peanut areas is 40%, with mean losses estimated at 38% when GRSV is present and 64% when there is the presence of virus and reduction in plant density. Michelotto, M. D. et al. notas de sintomas visuais. Pelos resultados obtidos, constatou-se que a espécie de vírus predominante é Groundnut ringspot tospovirus (GRSV). Conclui-se que quanto menor o estande maior a percentagem de plantas com sintomas da virose. A incidência do GRSV nas áreas comerciais de amendoim é em média de 40% sendo as perdas médias estimadas em 38% quando há a presença do GRSV e em 64%, quando há a presença do vírus e a redução na densidade de plantas. Palavras-chave: Arachis hypogaea L. Incidência. Produtividade. Severidade. Tospovirus.

We report the first full-length genome of a Bougainvillea chlorotic vein banding virus, isolate BCVBV-UNB-01, causing leaf yellowing in a Bougainvillea spectabilis from Brasília, Brazil. The genome, recovered using high throughput sequencing (Illumina HiSeq) and Sanger, consisted of 8665 nucleotides and four typical badnavirus ORFs: ORF I with 456 nt in length, ORF II with 432 nt, ORF III with 6636 nt and ORF IV with 594 nt. Phylogenetic analysis using Bayesian inference of the 1228 bp of the RT + RNase H region along other 35 badnaviruses clustered isolate BCVBV-UNB-01 with BCVBV accession (NC011592) from Taiwan. The accurately aligned region of 1228 bp using Sequence Demarcation Tool (SDT) software, confirmed this result, evidencing a robust identification. In addition, further studies involving biological characteristics, distribution and diversity of BCVBV in Brazil will be conducted in an attempt for better understanding the role of interactions among virus, plant and vector.

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