Presence of Potyvirus in the Norte de Santander department and molecular characterization of NIb protein in Colombian SCMV isolates

Potyviruses are the largest genus of plant viruses that cause significant losses over a wide range of crops. In this paper, the presence of potyvirus in different plant crops in the provinces of Ocaña and Pamplona located in the north and south of the Department of Norte de Santander (Colombia) was evaluated with RT-PCR analysis using universal oligonucleotides specific to the region that encodes the NIB protein. The results indicate the presence of several potyvirus in Pamplona in economically important crops such as corn (Zea mays), tomato (Solanum lycopersicum), potato (Solanum tuberosum) and zucchini (Cucurbita pepo). In Ocaña, potyvirus was found in bean (Phaseolus vulgaris), corn and pumpkin (Cucurbita maxima). In corn, one of the most important crops, the presence of the Sugarcane mosaic virus (SCMV) was confirmed with nucleotide sequencing. This is the first report of this virus in the department. The presence of several potyviruses in different crops in Norte de Santander indicate an alarming phytosanitary condition that must be addressed with priority to establish detection and control systems that maximize production, ensure agricultural sustainability, and propose certification schemes and improvement programs to reduce economic losses. Additional key words: Potyvirus; molecular diagnosis; phytopathology; plant virus. 1 Universidad Francisco de Paula Santander, Grupo de Investigación Fitobioquímica y Biología Molecular (FITOBIOMOL), San Jose de Cucuta (Colombia). ORCID Chaves-Bedoya, G. : 0000-0003-1013-614X; ORCID Ortíz-Rojas, L.Y. : 0000-0002-0818-3089 2 Corresponding author: gchavesb@ufps.edu. co Doi: https://doi.org/10.17584/rcch.2021v15i2. 12481 rEVIStA COLOMBIANA DE CIENCIAS HOrtÍCOLAS Vol. 15 No. 2, e12481, May-August 2021 e-ISSN: 2422-3719 · ISSN-L: 2011-2173 The potyviruses (genus Potyvirus family Potyviridae) is made up of 175 species (ICTV 2020). This viral genus, non-persistently transmitted by more than 200 species of aphids, has a great capacity for adaptation to new environments and hosts and can infect monocotyledonous and dicotyledonous plants, including crops and wild plants (Nigam et al., 2019). Among the virus genera that infect plants, potyviruses are the most studied from the point of view of the functional characterization of their proteins, interaction with the host, evolution, taxonomy and diagnosis (Revers and Garcia, 2015). They have a flexuous particle that is 700-750 nm long, and their genome consists of a single strand of RNA with approximately 10,000 nucleotides with positive polarity. This potyvirus encodes a large polyprotein that undergoes proteolytic processing, providing essential functions for replication and movement. In the 5’à3’ direction, the proteins encoded by the potyviruses are P1, HCPro, P3N-PIPO, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP. Among these proteins, NIb is an RNA dependent RNA polymerase or replicase whose function is viral genome replication (Hong and Hunt, 1996). The NIB genome sequence is well preserved and has been used for the design of universal primers for the detection of potyviruses (Ha et al., 2008; Zheng et al., 2010). New species of potyvirus are identified every year. By 2019, 167 species had been reported (Nigam et al., 2019). By mid-2020, 175 species had already been identified (ICTV, 2020). The data confirmed that this genus is one of the more important groups of viruses that represent an economic risk and a threat to crops around the world. Most diseases caused by potyviruses have symptoms such as mosaics, speckles, chlorotic rings or discoloration and deformation in foliage, flowers, fruits and stems, and necrosis of various tissues. Most cause severe delays in young plants and drastically reduce yields (Agrios, 2005). The severity of losses is proportional to the time the plant has been infected, i.e. how young the plant was when infected (Revers and Garcia, 2015). Diagnosis of viral diseases can be addressed from different approaches, ranging from symptomatology in indicator plants, electron microscopy techniques, enzyme assays such as ELISA tests, and molecular methods including Polymerase Chain Reaction (PCR). The latter is the main route of identification and diagnosis in potyviruses (Díaz et al., 2010). rESUMEN Los potyvirus son el género más grande de virus de plantas que ocasionan pérdidas significativas en un amplio rango de cultivos. En este trabajo mediante análisis de RT-PCR con oligonucleótidos universales específicos para la región que codifica la proteína NIb, se evaluó la presencia de potyvirus en diferentes plantas de cultivo en las provincias de Ocaña y Pamplona ubicados al norte y sur del departamento de Norte de Santander respectivamente. Los resultados indican la presencia de potyvirus en la provincia de Pamplona en plantas de importancia económica como maíz (Zea mays), tomate (Solanum lycopersicum), papa (Solanum tuberosum) y calabacín (Cucurbita pepo); y en la provincia de Ocaña en plantas de frijol (Phaseolus vulgaris), maíz y ahuyama (Cucurbita maxima). En maíz se confirmó mediante secuenciación nucleotídica la presencia del virus del mosaico de la caña de azúcar (SCMV), por lo que este se constituye el primer reporte de este virus en el departamento. Los resultados positivos por RT-PCR de la presencia de potyvirus en diferentes cultivos en Norte de Santander indican la necesidad apremiante de establecer sistemas de detección y control que permitan maximizar la producción, asegurar la sustentabilidad agrícola, proponer esquemas de certificación y programas de mejoramiento para reducir las pérdidas económicas. Palabras clave adicionales: Potyvirus; diagnóstico molecular; fitopatología; virus vegetal. received: 11-02-2021 Accepted: 30-04-2021 Published: 18-05-202