Nucleotide sequence analysis of Plum pox virus isolate W3174:: Evidence of a new strain

The nucleotide sequence of Plum pox virus (PPV) isolate W3174 was determined. The virus genome consists of 9788 nucleotides (m), excluding the poly(A) tail at the 3'-terminus, with 5'- and 3'-untranslated regions (UTRs) of 146 and 219 nt, respectively. The deduced polyprotein consists of 3 141 amino acid (aa) residues, with the coat protein region consisting of 993 nt (331 aa). In comparisons with PPV-D, -M, -EA and -C isolates, nucleotide identity levels ranged from 79 to 80% for the entire genome and from 78 to 79%, 78 to 81%, and 92 to 95% for the NIb, CP, and 3'-UTR regions, respectively. The majority of nucleotide substitutions in the NIb region of W3174 are silent, while substitutions in the CP region are not silent, giving aa identities of 89-91% and 79-81%, respectively. The HC-Pro region contains the KITC and PTK motifs, and the DAG motif is located at positions 12-14 of the deduced CP aa sequence, all associated with aphid transmission. Phylogenetic analysis based on the complete genome sequence, the NIb, CP, and 3'-UTR region were performed. PPV-W3174 consistently formed a distinct clade or group, when compared to members of all four recognized strains of PPV, indicating that it is genetically distinct. These results are consistent with serological and nucleic acid-based strain typing data and justify recognition of this isolate as representative of a new strain identified as PPV-W. (c) 2005 Elsevier B.V. All rights reserved.