Molecular characterization of Apple necrotic mosaic virus identified in crabapple (Malus spp.) tree of China

Apple necrotic mosaic virus (ApNMV) was identified in crabapple trees with mosaic symptoms from Zaozhuang, Shandong Province, China, by reverse transcription polymerase chain reaction (RT-PCR) analysis. The complete nucleotide sequences of one isolate from crabapple (ApNMV-Hai) and two isolates from apple (ApNMV-Hua and -Qu) were determined. The sizes of genomic RNA1, 2 and 3 of the three isolates differed from those of the previously reported isolate ApNMV-P126 from Japanese apple, especially RNA3. Compared with the nucleotide (nt) sequence of RNA3 in isolate P126, those in the Hai and Qu isolates were 7 and 33 nt shorter, respectively, and that of isolate Hua was 7 nt longer. Alignment analyses showed that these differences in size were mainly due to differences in the lengths of the 5' untranslated region (UTR) and the UTR region between the ORFs encoding the movement protein and the coat protein. In the phylogenetic trees constructed using the full genomic sequences of RNA1, 2 and 3, the isolate Hai clustered into a group with the isolate Qu in the RNA1 tree, but formed an individual branch in the RNA2 and 3 trees. Three recombination events were identified in the nucleotide sequences of RNA1 and 2 among the isolates ApNMV-Hai, -Hua, and -Qu. This is the first report of the full genome sequence of ApNMV in crabapple.