Molecular characterization of four citrus tristeza virus isolates that cause severe symptoms in navel orange in Ganzhou, China

In the present study, complete genome sequences of four citrus tristeza virus (CTV) isolates that cause severe stem pitting in Newhall navel orange (citrus sinensis) in Ganzhou, Jiangxi Province, China, were determined by transcriptome sequencing. The obtained sequence alignments showed that at the whole genome level, the four CTV isolates shared 79.18-99.63% nucleotide identity with 80 CTV isolates previously reported from around the world. Phylogenetic analysis revealed that the CTV isolates 2019-30-2, 2019-30-3, 2019-6-DY, and 2019-7-DY were grouped into RB, T3, VT, and RB genotypes, respectively. Recombination analysis indicated that the four CTV isolates are recombinants and may have originated through multiple recombination events in which parts of their genomes were exchanged between divergent CTV sequences.