Molecular characterization and detection of recombinant isolates of potato virus Y from China

Although potato virus Y (PVY) is one of the most economically important pathogens of potatoes in China, few studies have been carried out to characterize the virus in that country. Using reverse transcription-polymerase chain reaction (RT-PCR)-based genotyping developed previously, two types of recombinant PVY were identified in China for the first time. One resembled the European (Eu) type of potato tuber necrosis strain (Eu-PVY^NTN), possessing three widely recognized recombinant joints (RJs 1–3) of the common strain (PVY^O) and the Eu- type tobacco veinal necrosis strain (Eu-PVY^N). The other, on the other hand, appeared to have only RJ1 and RJ2. The complete genome of a representative isolate, PVY-HN2, from the second type was subsequently sequenced. Comparison of the sequence of ‘HN2’ with those of PVY^O and Eu-PVY^N not only confirmed the recombinant nature of ‘HN2’ but also revealed the existence of three recombinant events in the isolate, similar to that in PVY^NTN-Hun. However, the two isolates differed significantly at RJ1 (PVY^NTN-Hun vs. HN2, nt 2419 vs. nt 2521) and RJ3 (PVY^NTN-Hun vs. HN2, nt 9183 vs. nt 8572) and slightly at RJ2 (PVY^NTN-Hun vs. HN2, nt 5844 vs. nt 5867). A primer pair was developed to facilitate the detection of the alternative RJ3. Using the newly and previously designed RJ primers, all targeted RJs were detected. Interestingly, tests of the available PVY samples indicated that two were doubly infected with both types of recombinant PVY, further confirming the effectiveness of the detection. Further analysis of these samples using enzyme-linked immunosorbent assay and bioassay revealed that ‘HN2’ possesses a PVY^O serotype, a PVY^N pathotype in tobacco and a PVY^NTN pathotype in potato.