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Two Chinese isolates of Citrus tristeza virus (CTV) from Poncirus trifoliata, designated as CN-L1-ZT1 and CN-M1-ZT1, were completely sequenced. The phylogenetic analysis of these isolates suggested that two novel CTV genotypes L1 and M1 should be considered. In addition, the recombination analysis indicated that most of the 3′ terminal p33 to p23 open reading frames (ORFs) of these isolates were derived from different unknown CTV isolates. Thus, the L1 and M1 genotypes were two recombinants distinct from known CTV genotypes. RT-PCR protocols developed based on the p33 regions facilitated genotyping of L1 and M1 from other major CTV genotypes in China. These results could play an important role in further study of global CTV diversity and evolution.

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