A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages.

A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small ß1/ß5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep ß1/ß5 sheet region determines specificity of this protein for DNA replication origin sequences.

A new strain of tomato severe leaf curl virus and a unique variant of tomato yellow leaf curl virus from Mexico.

The complete genome sequence of a distinct variant of tomato yellow leaf curl virus-Israel (TYLCV-IL) and the DNA-A sequence of a new strain of tomato severe leaf curl virus (ToSLCV) isolated in San Luis Potosi, Mexico, are described and analyzed. The TYLCV-IL[MX:SLP:11] variant differs from all TYLCV-IL isolates described so far by a unique 42-nt duplicated sequence comprising a part of the conserved stem-loop element of the virion-strand replication origin and adjacent regulatory sequences. TYLCV-IL[MX:SLP:11] was associated with tomato chino La Paz virus (ToChLPV-B[MX:SLP:11]) in a Solanum pimpinellifolium plant, and with pepper huasteco yellow vein virus (PHYVV-[MX:SLP:11]) and ToSLCV-GT[MX:SLP:11] in a Solanum lycopersicum plant. In addition, a distinct ToSLCV exhibiting low sequence identity (<89 %) to other ToSLCV isolates from Mexico was found in a tomato plant collected in the same field. Sequence analysis of this new ToSLCV strain indicates that it is a recombinant of close relatives of ToSLCV-GT[MX:SLP:11] and ToChLPV-B[MX:SLP:11] found in mixed infections with TYLCV-IL[MX:SLP:11].

First Report of Tomato yellow leaf curl virus Co-infecting Pepper with Tomato chino La Paz virus in Baja California Sur, Mexico.

Chile peppers are among the most common and important crops in the State of Baja California Sur, Mexico, where diverse varieties of this crop are annually cultivated. The "chile ancho" (Capsicum annuum L. var. ancho poblano) is one of the most popular hot peppers that is exported fresh to the United States. During a survey in December of 2007 in an experimental field of the CIBNOR in El Carrizal, one of the principal farm districts in the state, a high incidence of yellowing, stunted growth with shortened internodes, foliage discoloration, malformation and crinkle, abortion of flowers, and reduction in size and quantity of fruit were noted in chile ancho. Symptoms and the presence of large populations of whiteflies in the field suggested a possible viral etiology of disease. The symptoms of disease were successfully transmitted by grafting from field plants to tomato and pepper test plants. Samples from both field and test plants were analyzed by scanning electron microscopy (SEM) and molecular techniques. SEM study revealed groups of geminate particles characteristic of begomoviruses (Geminiviridae) in phloem tissue of randomly selected symptomatic plants (four field and two test plants). Total DNA from 12 symptomatic plants (eight naturally infected and four test plants) was obtained by a modified Dellaporta method and analyzed by PCR using the begomovirus universal primers prRepDGR (2) and prC889 (3). Amplicons of ~1.4 kb were obtained from all plant samples and PCR products from four of them were cloned into pGEM-T Easy vector (Promega, Madison, WI) and subsequently analyzed by restriction fragment length polymorphism (RFLP) using EcoRI and HinfI. Two distinct restriction fragment patterns were observed among the cloned PCR products, indicating the occurrence of at least two viruses in the infected plant tissues. The four examined samples contained the same two begomoviruses according to the RFLP analysis data. The complete sequence of the genomic component A of those viruses was determined by PCR amplification of viral DNA with universal, degenerate primers previously described (2), the subsequent cloning of overlapped PCR products, and sequencing. The full-length DNA-A sequence was assembled and compared with viral sequences available at the GenBank database using BlastN and the ClustalV alignment method (MegAlign; DNASTAR, Madison, WI). The 2,781-bp complete genome sequence of one co-infecting monopartite begomovirus (Accession No. HM459851) displayed the highest identity (99%) with Tomato yellow leaf curl virus (TYLCV), isolate Guasave, Sinaloa (Accession No. FJ609655). The 2,609-bp DNA-A sequence of the second begomovirus exhibited the highest nucleotide identity (96%) with Tomato chino La Paz virus (ToChLPV)-[Baja California Sur] (Accession No. AY339619). The presence of TYLCV in this region of Mexico had not been previously reported nor was ToChLPV detected in pepper until now. To our knowledge, this is the first report of a mixed infection of pepper plants with TYLCV and a bipartite begomovirus in Baja California Peninsula. Since the high frequency of recombination events observed in begomovirus mixed infections involving TYLCV (1), it would be important to monitor the possible emergence of ToChLPV-TYLCV recombinants with higher potential virulence. References: (1) S. García-Andrés et al. Virology 365:210, 2007. (2) A. Mauricio-Castillo et al. Plant Dis. 91:1513, 2007. (3) S. D. Wyatt and J. K. Brown. Phytopathology 86:1288, 1996.