Molecular characterization and potential sources of Citrus tristeza virus in Oman

A study was conducted to characterize occurrence, molecular variability and potential sources of Citrus tristeza virus (CTV) in Oman. A survey during 2009 and 2010 showed that CTV occurs in most (91%) of the surveyed districts. Moderate to high levels of infection with CTV in lime were detected in northern Oman (15-63%) compared to the south (0-12%). This could be related to the continuous introduction of infected citrus germplasm in the north from abroad, where CTV was detected in 45% of citrus seedlings imported from Syria, Lebanon, India, Pakistan and Egypt. CTV was detected for the first time in sweet lime, sweet lemon, citron, mandarin, sweet orange and sour orange and was found to be associated with stem pitting, stunting, leaf curling and vein clearing symptoms in many of the infected trees and seedlings in Oman. Bi-directional reverse transcription-PCR analysis of the coat protein (CP) gene of 22 randomly selected CTV-positive samples provided evidence that severe strains of CTV exist in Oman. Cloning and sequencing the CP gene of six isolates showed that they have 91-100% nucleotide identity with each other and 96-99% with representative isolates from other parts of the world. Phylogenetic analysis of the CTV isolates showed that four belong to CTV Group 4. However, two isolates formed a separate clade with 100% bootstrap support for separation from Group 5. Phylogenetic analysis and coefficient of differentiation values suggest that the two isolates from Oman constitute a new CTV phylogenetic group.