Mauricio Marín

Potato yellow vein virus (PYVV; Crinivirus flavisolani) is a major limiting virus in potato production in Colombia and other South American countries. This virus is transmitted by both seed tubers and the whitefly Trialeurodes vaporariorum. While PYVV has also been reported in naranjilla, cape gooseberry, and tomato, its epidemiology in these solanaceous species remains poorly understood. Unlike potatoes, these crops are propagated by sexual seeds and are commercially distributed as seedlings. This study evaluated the presence of PYVV in tomato crops from various departments in Colombia using RT-qPCR with different tissues including leaves, fruit pericarp, seeds, and seedling shoots. The genomic identity of the virus was confirmed through high-throughput sequencing (HTS) of leaf samples from the Chonto tomato variety. A seed-to-seedling transmission assay was also conducted using surface-disinfected seeds cultured in vitro on MS medium. The virus was detected in 75% of fruit samples, 35% of leaf samples, and 40% of seedling shoot samples, but only in 10% of non-commercial seeds and none of the commercial seeds. HTS enabled assembly of the nearly complete viral genome with high sequencing depth. The in vitro assay indicated that PYVV has a low-frequency seed-to-seedling transmission in tomato, suggesting that disease management strategies should prioritize control of the whitefly vectors.

Tomato ( Solanum lycopersicum ) and bell pepper ( Capsicum annuum ) are vital crops in Colombia and other countries, but their production faces threats from Tobamovirus fructirugosum (ToBRFV), a virus causing significant yield and quality losses globally. Although it was previously reported in Antioquia, Colombia, its nationwide distribution and presence in bell peppers remained largely unknown. We surveyed tomato and bell pepper crops throughout Colombia and examined the prevalence, genetic diversity, and potential transmission routes of ToBRFV. To identify the most likely ToBRFV transmission routes, we developed a spatial network model representing connectivity among S. lycopersicum and/or C. annuum production areas and applied network analysis to identify municipalities of epidemiological importance. Using RT‐qPCR, Sanger sequencing, and HTS, we detected ToBRFV in tomato fields across multiple provinces and confirmed its first presence in Colombian bell pepper crops. Screening revealed a widespread presence in seeds and plantlets, indicating that infected material is a key component in disease transmission. On the other hand, genome sequencing of a bell pepper isolate provided the most complete Colombian ToBRFV genome. Phylogenetic analysis showed multiple introductions and a new Colombian lineage. Analysis of host resistance loci showed that the Tm‐1 and Tm‐2 alleles present in Chonto and Cherry varieties are unlikely to confer effective resistance to ToBRFV, consistent with the observed susceptibility. Spatial modelling identified key transmission routes and high‐risk areas, especially in the Andean region. This work is the first comprehensive detection of ToBRFV in Colombian tomato and bell pepper and highlights priority areas for surveillance and control.

El tomate (Solanum lycopersicum L.) es uno de los cultivos de mayor importancia mundial, con una producción cercana a 180 Mt/año. En la última década, este cultivo se ha enfrentado al surgimiento del tobamovirus Tomato brown rugose fruit virus (ToBRFV), que se ha dispersado a los cinco continentes a causa de su eficiente transmisión mecánica y por semillas. En este trabajo se evaluó la presencia de este virus en Colombia utilizando RT-LAMP en 15 muestras de semillas de diferentes variedades procedentes de frutos comercializados en supermercados del país. Además, la ocurrencia del ToBRFV se confirmó mediante secuenciación Sanger de amplicones generados por RT-PCR convencional y en tiempo real. Los resultados de las pruebas RT-LAMP indicaron la presencia del ToBRFV en las 15 muestras evaluadas, la cual confirmó su identidad por RT-PCR y secuenciación de los productos de ~200 pb obtenidos con el par de primers F3/B3, así como de productos de ~800 y ~150 pb con los primers Tob-Uni_1/Tob-Uni_2 y ToBrFV_qs1/Tob-Uni_1, respectivamente. Los árboles filogenéticos obtenidos a partir de los análisis de las secuencias agruparon los aislamientos colombianos en el clado general mundial de esta especie viral, con muy altos niveles de identidad (>99 %). Finalmente, las pruebas de RT-qPCR también confirmaron la presencia del ToBRFV, el cual fue el primer registro de este virus en Colombia. Dado el riesgo que presenta la enfermedad causada por ToBRFV sobre los rendimientos y calidad de los frutos de tomate, es necesario que la cadena hortofrutícola del país implemente urgentemente medidas fitosanitarias para su manejo.

Viruses are a significant threat to tomato crops (Solanum lycopersicum) worldwide. In Colombia, 20 species of viruses from 10 genera have been reported in tomato, with 9 of them being RNA viruses that cause varying levels of damage. This study in Antioquia evaluated the presence of three RNA viruses: potato virus Y (PVY), potato yellow vein virus (PYVV) and Southern tomato virus (STV) in different tomato seeds and plants using RT-qPCR, conventional RT-PCR and Sanger sequencing. The study included 15 leaf tissue samples of the Chonto variety and 15 seed samples of various tomato varieties (Cherry, Chonto, Yellow, Kidney, San Marzano, and Mexican husk tomato). The results showed high levels of PVY in leaf tissue (93.3%) and seeds (46.6%), while PYVV was detected in 60% of leaf samples and 26.6% of seed samples. STV was found in 93.3% of seeds but was not detected in any leaf samples. Sanger sequencing confirmed the presence of these viruses, and phylogenetic analyses placed the isolates in clades previously reported for these viruses in Colombia. These findings underscore the need for a tomato seed certification program in Colombia to ensure viral-free seeds.

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.

La uchuva es una de las frutas promisorias para la zona andina de Colombia gracias a su alta demanda internacional. En Antioquia, su siembra se concentra en el oriente, aunque otras subregiones como el norte y suroeste presentan condiciones óptimas para su cultivo. Ya que las enfermedades de origen viral son uno de los problemas emergentes de este frutal, en este estudio se evaluó la infección de virus de RNA que infectan los cultivos de uchuva en el suroeste de Antioquia. Para esto se utilizaron pruebas de RT-qPCR en muestras foliares de plantas sintomáticas y asintomáticas obtenidas en ocho lotes, así como en ocho muestras de semillas extraídas de frutos comercializados en esta subregión. Los resultados indicaron la presencia en al menos una muestra foliar de los virus PVY, PVX, PVS, CGIV-1 y PMTV, mientras que PVV, PYVV y PhyVNV no fueron detectados. El PMTV (75 %) y el PVX (62.5 %) fueron los virus que presentaron mayores niveles de prevalencia en muestras sintomáticas y asintomáticas, respectivamente. Para el caso de las semillas, se encontró la infección de los virus PVX (87.5 %), PVS (75 %), PVY (37.5 %), PhyVNV (12.5 %) y CGIV-1 (12.5 %). Adicionalmente, mediante análisis de NGS se detectó la presencia de secuencias de los virus CMV, PhyVNV, PVS, y TaLMV. Estos hallazgos señalan la necesidad de establecer en el país programas de monitoreo de virus en cultivos de uchuva y de certificación de semilla.

The productivity of potato in Colombia is far from its full potential mainly due to the high prevalence of viruses in seed-tubers. To gain a deeper insight into the health status of S. tuberosum and S. phureja seed-tubers used by farmers in the province of Antioquia (Colombia), we have investigated the prevalence of PVY, PVV, PVS, PVX, PRLV, PYVV, PMTV and PVB in certified and uncertified seed lots. The presence of viruses was determined by RT-qPCR, RT-PCR, Sanger and High-Throughput Sequencing (HTS). The eight viruses were detected in at least one lot sample of S. tuberosum or S. phureja and for most of the viruses, no significant differences in prevalence were observed between certified and uncertified seed-tuber lots; however, the number of co-infecting viruses and viral loads seem to be lower in the certified seeds. These results confirm the urgent need to improve current seed-tuber production standards in Colombia.