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Potato virus S (PVS) (genus Carlavirus , family Betaflexiviridae ) is one of the most prevalent viruses in potato crops ( Solanum tuberosum and S. phureja ) around the world, causing reductions in crop yields between 10 and 20 %. Symptoms of PVS infection may include leaf mottling, rugosity of leaves, deepening of the veins and reductions in crop yields between 10 and 20 %. Virions are flexuous rods of 610-710 nm with a positive-sense ssRNA genome of approximately 8500 nt comprising six ORFs, a 5′CAP and a 3′poly-A tail. PVS has been classified into two groups: PVS O (Ordinary) and PVS A (Andean). PVSA induces severe symptoms in infected plants, such as premature senescence and defoliation, and is more efficiently transmitted by aphids than PVS O . To date, only five PVS genomes have been completely sequenced, including those of three PVS O and two PVS A strains. Currently, there are no reports of complete PVS genome sequences from Andean South America. In this work, we present the complete genomic sequence of a novel PVS strain infecting S. phureja that is clearly distinct from currently known PVS isolates.

Viral diseases are among the most limiting factors in the production of potato in Colombia and the rest of the world. The best strategy to control plant viruses consists on the use of certified seed tubers, control of arthropod vectors and the use of adequate crop management practices that reduce mechanical transmission and the presence of viral reservoirs like weeds and volun-teer plants. However, the successful implementation of these practices relies on the availability of highly sensitive techniques that allow for the asymptomatic detection of viruses. In this work, we tested the performance of Next-generation sequencing (NGS) and real time RT-PCR (RT-qPCR) on a single volunteer potato plant (cv. Diacol-Capiro) growing naturally in a seed-tuber storage facility in Yarumal (Antioquia). Our NGS results demonstrate a mixed infection with Potato virus Y (PVY) and Potato leafroll virus (PLRV). RT-qPCR was performed in roots, main stolons, crown (root collar) and upper, middle and lower leaves using specific primers for PVY, PLRV, Potato virus S (PVS), Potato virus V (PVV), Potato virus X (PVX) and Potato yellow vein virus (PYVV). Only PVY and PLRV were detected in good agreement with the NGS data. This work demonstrates the use-fulness of both techniques for supporting integrated management of plant viruses in potato, in-cluding virus detection in natural reservoirs such as volunteer plants and weeds.

As part of an initiative to characterize viruses infecting Cape gooseberry in the province of Antioquia (Colombia), we report the genome sequence of a new member of the genus Ilarvirus (family Bromoviridae ). This virus was identified in a Cape gooseberry plot in the municipality of Marinilla in a mixed infection with potato virus Y (PVY) as part of high-throughput sequencing initiative. Results were confirmed by nested RT-PCR and DAS-ELISA. Phylogenetic analysis suggested that the Cape gooseberry ilarvirus is a new member of subgroup 1 and it is most closely related to ageratum latent virus (AgLV). The name “Cape gooseberry ilarvirus 1” (CGIV-1) is proposed for this new ilarvirus.

Spongospora subterranea, the causal agent of Potato powdery scab, is an important soil-borne obligate protozoan commonly found in Andean soils. This is a serious problem that causes cosmetic damage on the skin of tubers and induces root gall formation, diminishing the yield and commercial value of the potato. Genetic studies on S. subterranea are difficult due to its obligate parasitism, which explains the lack of available knowledge on its basic biology. S. subterranea is a member of the Plasmodiophorida order, a protist taxa that includes other important plant pathogens such as Plasmodiophora brassicae and Spongospora nasturtii. Little is known about the genomes of Plasmodiophorida; however, with the use of Next-Generation Sequencing technologies combined with appropriate bioinformatic techniques, it is possible to obtain genomic sequences from obligate pathogens such as S. subterranea. To gain a better understanding of the biology of this pathogen and Plasmodiophorida in general, DNA sequences from a cystosori-enriched sample of S. subterranea were obtained using 454 pyrosequencing technology. As a first step in understanding the nutritional requirements of S. subterranea as well as its infective and resistance structures, we present a bioinformatic analysis of 24 contigs related to genes involved in the glycolysis, starch, celullose and chitin metabolism. Intron structure and codon usage is also discussed. The genes analyzed in this study are a good source of information for studies aimed at characterizing these enzymes in vitro, as well as the generation of new methods for the molecular detection of S. subterranea in either soils or infected plants.

Las virosis son uno de los problemas fitosanitarios más limitantes para la producción de papa, siendo los virus Potato leafroll virus (PLRV), Potato virus Y (PVY), Potato virus S (PVS) y Potato ye-llow vein virus (PYVV) los que generan mayores pérdidas económicas en la región andina. Gene-ralmente estos virus son transmitidos por insectos hemípteros y por tubérculos-semilla. En esta investigación se evaluó la presencia y distribución del PLRV en tubérculos de Solanum tuberosum variedad Diacol-Capiro y S. phureja variedad Criolla-Colombia obtenidos en Antioquia, utilizando pruebas serológicas y moleculares. Mediante DAS-ELISA se evaluaron 128 muestras consisten-tes en tres tipos de tejidos (piel, yemas latentes y brotes), mientras que con RT-PCR en tiempo real (RT-qPCR), se utilizó un subgrupo de 12 muestras de cada variedad. Utilizando DAS-ELISA, el PLRV se encontró en el 3,1% y 10,1% de las muestras de Diacol-Capiro y Criolla-Colombia, respectivamente; siendo evidente una mayor detección del virus en la piel de los tubérculos de ésta última variedad. Las pruebas de RT-qPCR detectaron el PLRV en 83,3% y 91,6% de las 12 muestras de Diacol-Capiro y de Criolla-Colombia, respectivamente; con valores de Ciclo umbral (CT) entre 17,72 y 30,59. La naturaleza de los amplicones obtenidos por RT-qPCR fue confirmada por secuenciación como parte de una región codificante de la cápside del PLRV (Identidad=99%-100%). Estos resultados enfatizan en la necesidad de utilizar tubérculo-semilla certificados por su sanidad viral en los cultivos de papa del país y de fortalecer dichos programas a partir del empleo de técnicas de detección altamente sensibles como RT-qPCR.

Transcriptome analysis of chili and bell pepper samples from commercial plots in the municipalities of Santa Fe de Antioquia and El Peñol in the province of Antioquia revealed the presence of viral sequences with significant similarity to genomes of members of the genus Endornavirus. Assembly of the chili and bell pepper transcriptomes resulted in consensus sequences of 14,727 nt and 14,714 nt that were identified as Bell pepper endornavirus (BPEV). Both sequences were nearly identical by 99.9 % at both nucleotide and amino acid levels. The presence of BPEV was confirmed by RT-qPCR, RT-PCR and Sanger sequencing using RdRp-specific primers designed from the assembled sequences in ten independent random samples taken from the investigated bell pepper stands. The phylogenetic analysis of both BPEV variants and their affiliation within the genus Endornavirus is discussed. For our knowledge, this is the first study on this group of viruses in Colombia.

Tomato leaf curl New Delhi virus (ToLCNDV) represents a threat to economically important horticultural crops. A real-time loop-mediated isothermal amplification (LAMP) assay for in-field ToLCNDV detection was developed, coupled to a rapid sample preparation method, and tested both in field and laboratory conditions on zucchini squash, tomato, and pepper samples. A set of six LAMP primers was designed for specific ToCLNDV detection, targeting a 218-nucleotide sequence within the AV1 gene. The sensitivity, specificity and accuracy of the real-time LAMP assay and comparison with canonical PCR were evaluated. The real-time LAMP assay developed was about one-thousand times more sensitive than the conventional PCR method, detecting a total of 4.41 × 102 genome copies as minimum target; no cross-reactivity was detected with the other geminiviruses used as the outgroup. The rapid sample preparation method allows for a reliable detection with a low reaction delay (≈2–3 min) compared to canonical DNA extraction, providing results in less than 45 min. Lastly, an increase in ToLCNDV-positive sample detection was observed compared to PCR, in particular for asymptomatic plants (85% and 71.6%, respectively). The real-time LAMP assay developed is a rapid, simple, specific, and sensitive technique for ToLCNDV detection, and it can be adopted as a routine test, for both in-field and laboratory conditions.

Purple passion fruit (Passiflora edulis f. edulis), also known as gulupa, is a vine plant of the familiy Passifloraceae, which in recent years has gained importance in the world fruit market due to its exotic nature and excellent organoleptic properties. Although the demand for gulupa in Colombia has increased significantly to become one of the most important fruit exports, the cultivated area has been in decline since 2009 due to the impact of plant diseases. Cucumber mosaic virus (CMV), soybean mosaic virus (SMV) and cowpea aphid borne mosaic virus (CABMV) are amongst the main viruses found infecting gulupa in Colombia. To further characterize the virome of gulupa, a deep sequencing transcriptome study was performed from a producing region in eastern Antioquia. Based on the results of next-generation sequencing (NGS), we report the genome sequence of a tymovirus infecting this plant. Phylogenetic analysis revealed this virus to be a close relative of Passion fruit yellow mosaic virus (PFYMV), Cassia yellow mosaic-associated virus (CYMaV) and Calopogonium yellow vein virus (CYVV). To date, only a 1115 nt segment comprising the RdRP-CP region of PFYMV has been reported; this sequence shares 84.79% and 95.24% identities at the nucleotide and amino acid levels with the purple passionfruit tymovirus suggesting that the detected virus is a PFYMV isolate (PFYMV_Antioquia). Finally, RT-qPCR and Sanger sequencing using specific primers confirmed the presence of PFYMV in different purple passionfruit crops in Antioquia. This is the first complete genome sequence of a PFYMV isolate reported in the world.

Transcriptome analysis of a Cape gooseberry ( Physalis peruviana ) plant with leaf symptoms of a mild yellow mosaic typical of a viral disease revealed an infection with Potato virus X (PVX). The genome sequence of the PVX-Physalis isolate comprises 6435 nt and exhibits higher sequence similarity to members of the Eurasian group of PVX (~95 %) than to the American group (~77 %). Genome organization is similar to other PVX isolates with five open reading frames coding for proteins RdRp, TGBp1, TGBp2, TGBp3, and CP. 5′ and 3′ untranslated regions revealed all regulatory motifs typically found in PVX isolates. The PVX-Physalis genome is the only complete sequence available for a Potexvirus in Colombia and is a new addition to the restricted number of available sequences of PVX isolates infecting plant species different to potato.

Due to the increase of the international demand for functional fruits, cape gooseberry (Physalis peruviana) has become one of the crops of highest expansion in Colombia and the Andean region of South America. nfortunately, the emergence of fungal and unidentified viral diseases has slowed down the cultivation of cape gooseberry in Colombia and, particularly, in the department of Antioquia. In this work, a next-generation sequencing virome analysis of cape gooseberry plants from eastern Antioquia was performed, using leaves exhibiting symptoms such as mosaics, leaf deformation and greening of veins. The complete genomes of Potato virus Y (PVY) and Potato virus V (PVV) were obtained in the assembled data. The presence of both viruses was confirmed in the samples obtained at two commercial cape gooseberry fields by real time RT-PCR (RT-qPCR) and partial Sanger sequencing of the coat protein (CP). Sequence analysis revealed significant sequence similarity between PVY and PVV isolates infecting P. peruviana to previously identified strains infecting potato (Solanum tuberosum and S. phureja) and tomato (Solanum lycopersicum) in the same geographical region. This study suggests that cape gooseberry could be an alternate host to viruses of other economically important solanaceous crops in the Andean region of South America.