title: Discrimination between mild and severe Citrus tristeza virus isolates with a rapid and highly specific real-time reverse transcription-polymerase chain reaction method using TaqMan LNA probes.
abstract: Severe isolates of Citrus tristeza virus (CTV) inducing seedling yellows (SY) and/or stem pitting (SP) in grapefruit or sweet orange are a major threat for the citrus industry worldwide. Identification of these CTV variants was achieved by quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) using a general primer set and three TaqMan locked nucleic acids (LNA) probes targeting sequences characteristic of severe, mild (non-SY, non-SP), and T36-like isolates. Successful amplification was achieved from fresh or silica-desiccated CTV-infected samples and all isolates but one reacted with one or more probes. Standard curves using RNA transcripts homologous to the three probes allowed a reproducible quantitative assay, with a wide dynamic range of detection starting with 10(2) copies. RT-PCR assays with homologous and heterologous transcript RNA mixes demonstrated that each probe reacted only with its cognate sequence which was detected even at ratios below 2.5%. Analysis of 56 pathogenically distinct CTV isolates from 20 countries showed that mild isolates reacted only with the mild probe, whereas severe SP and SY isolates reacted with the severe-SP or the T36-like probes, respectively, and often with a second probe. This procedure can be useful to identify and control potentially dangerous CTV isolates in areas affected only by mild isolates.
authors.affiliation: Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Moncada, 46113-Valencia, Spain.
authors.forename: S
authors.initials: S
authors.lastname: Ruiz-Ruiz
authors.forename: P
authors.initials: P
authors.lastname: Moreno
authors.forename: J
authors.initials: J
authors.lastname: Guerri
authors.forename: S
authors.initials: S
authors.lastname: Ambrós
mesh_terms: D002957:Citrus / Q000821:virology*; D017790:Closterovirus / Q000235:genetics / Q000302:isolation & purification / Q000472:pathogenicity*; D005838:Genotype; D054884:Host-Pathogen Interactions; D015341:Nucleic Acid Probes / Q000737:chemistry; D009841:Oligonucleotides / Q000737:chemistry; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D044366:Transition Temperature
chemical_list: D015341:Nucleic Acid Probes; D009841:Oligonucleotides; D012367:RNA, Viral; C477371:locked nucleic acid