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In 2009, a new citrus viral disease caused by Citrus yellow vein clearing virus (CYVCV) was first discovered in Yunnan province of China. In this study, a survey was conducted in 27 orchards from Yunnan province from April 2017 to September 2018. In all, 45 of a total of 513 citrus samples were tested positive for CYVCV by reverse transcription polymerase chain reaction (RT-PCR). Furthermore, the complete genome sequences of six CYVCV isolates from different hosts were sequenced. Comparisons of the whole genome sequences of these six CYVCV isolates as well as 34 isolates previously reported from around the world revealed the sequence identity ranged from 96.9% to 99.8% at nucleotide level, indicating that there is a very low level of sequence heterogeneity among CYVCV isolates of different hosts in Yunnan province. [ABSTRACT FROM AUTHOR]