A simplified RT-PCR-based detection of recombinant Plum pox virus isolates

Closely related natural Plum pox virus (PPV) isolates derived from homologous RNA recombination between PPV-D and PPV-M have been recently identified and shown naturally spread in several European countries. As their serological properties were identical with those of conventional PPV-M isolates, they could be detected only by combined analysis of at least two different genome parts. To simplify the detection of such recombinants primers specific to PPV-M and PPV-D sequences with binding sites located on both sides of the recombination crossover situated in the C-terminal part of NIb were designed. They were used for direct differentiation of PPV-M, PPV-D and their recombinants by reverse transcription-polymerase chain reaction (RT-PCR). This method is convenient for identification of a recombinant PPV in single as well as mixed infection with PPV-M or PPV-D.