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A putative new variant of citrus tristeza virus (CTV), JY-2, was identified in Chinese wild mandarin (Citrus daoxianensisS.W. He & G.F. Liu., syn. Citrus reticulataBlanco) by RT-PCR and high-throughput sequencing (HTS) of RNA sequencing (RNA-seq) data. The complete genomic sequence consisted of 19,112 nucleotides (nt). JY-2 shared the highest 89.4% of its genomic nt sequence, highest 90.4% of its ORF1a nt sequence, and highest 90.7% of its ORF1a amino acid sequence with CN-M1-ZT1. Phylogenetic analyses of complete genomic, ORF1a to ORF1b, and p33to p23nt sequences showed that JY-2 occupied a separate clade distinct from other existing CTV genotypes, suggesting that JY-2 is a new variant. RT-PCR analysis showed that JY-2 was exclusively found in Chinese wild mandarin trees from Jiangyong (Hunan Province). The current findings aid in understanding of the molecular diversity of CTV and give insights into its evolution.