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A previous study has identified two types of recombinant variants of  Potato virus Y  strain NTN (PVY NTN ) in China and sequenced the complete genome of the variant PVY NTN -HN2. In this study, the complete genome of isolate PVY NTN -HN1 was fully sequenced and analyzed. The most striking difference between the two variants was the location of recombinant joint three (RJ3). In PVY NTN -HN1, like other typical European-PVY NTN  isolates such as PVY NTN -Hun, the RJ3 was located at nucleotide (nt) 9183, namely the 3' proximal end of the CP gene (nt. 8571-9371), thus leading to most (the first 613 nucleotides from the 5' proximal end) of the CP gene (801 bp) with a PVY N  origin and PVY N -serotype; whereas in contrast, the RJ3 in PVY NTN -HN2 was located at nt 8572, consequently leading to a CP gene of PVY O  origin and PVY O -serotype. The varied genome composition among PVY O , PVY N , PVY N:O , PVY NTN -HN1 and PVY NTN -HN2 made them useful for the investigation of possible roles of gene segment(s) in symptom formation on host plants. When  Physalis floridana  plants were infected with different PVY isolates, two types of symptoms were induced. PVY N  and PVY NTN -HN1 induced mild symptoms (mainly mild mottling) whereas PVY O , PVY N:O  and PVY NTN -HN2 induced serve symptoms including leaf and stem necrosis, leaf-drop and stunting. These results, together with a previous study using artificial PVY chimeras, demonstrate that the CP gene, especially the 5' proximal segment (nt 8572-9183), and/or CP likely determine the pathogenicity of PVY in  P. floridana .

Differential pathogenicity of two different recombinant PVYNTN isolates in Physalis floridana is likely determined by the coat protein gene