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Citrus tristeza virus (CTV), the most devastating viral pathogen in citrus, causes tremendous economic losses to citrus industry worldwide.CTV isolates exhibit variable pathogenicities on their hosts indicating a mixed population of CTV in nature.Several fragments within the CTV genome have been used for studying the genetic diversity of CTV, however, the best region for rapid CTV strain differentiation is still absent at present.In present study, a systemic analysis was carried out to evaluate the best region within CTV genome for rapid CTV strain differentiation.