Apple Stem Pitting Virus (ASPV) is one of the most common viruses of apple and pear trees. During 2012 to 2013, a total of 1053 symptomatic and asymptomatic leaf samples were collected from orchards in nine provinces of Iran. ASPV infection was detected by DAS-ELISA and PCR in 54 samples (5.12%) from seven provinces. Based on the geographical origin, 22 representative isolates were selected for phylogenetic analysis. Twenty-two amplicons with a size of about 370 base pair (bp) comprising partial sequence of the Coat Protein (CP) coding regions of the viral genome were sequenced. Sequence data analysis, showed that the identities of 3'-terminal region of CP gene at both nucleotide and amino acid levels among the Iranian isolates were 95–100% and these isolates were closer to the Asian ASPV isolates than to the other isolates. Constructed phylogenetic tree by Neighbor-joining on the basis of the 3'-terminal region of CP gene sequences showed that the Iranian isolates were categorized into two major groups. Furthermore, phylogenetic and population genetic analysis were carried out on the basis of 3'-terminal region of CP gene which revealed that ASPV isolates were not geographically resolved. Also, all values in the GABranch analysis showed a ratio of substitution rates at Non-synonymous and Synonymous sites (dN/dS) below one, suggesting strong negative selection forces during C-terminal region of the ASPV CP gene history. To the best of our knowledge, this is the first report of distribution and partial genome sequence analysis of the ASPV in Iran.
