Characterization and genetic variability of coat protein gene of Apple chlorotic leaf spot virus isolates from apple in Kurdistan and western Azarbaijan Provinces, Iran

In this study, 174 leaf samples from main apple growing areas in Kurdistan and western Azarbaijan Provinces were examined for infection by Apple chlorotic leaf spot virus (ACLSV). The result of RT-PCR showed that 17 samples (9.7%) were infected by ACLSV in both provinces. Subsequently, the genetic structure of ACLSV was determined based on the full coat protein (CP) sequences of eight isolates from this study and those recently published from Iran and worldwide. In phylogenetic analysis, ACLSV isolates from apple clustered into three known phylogenetic types; B6, P205, and SHZ, which are characterized by three amino acids at positions of 40, 75 and 79. The new Iranian ACLSV isolates showed the CP amino acid sequence of Ser40-Tyr75-Glu79 which placed them with the B6 type. Further analyses showed that the Iranian ACLSV isolates (the new and previously published isolates) had lower genetic variability compared to isolates from other countries except for Brazilian population. Most of the CP codons were under negative selection (dN/dS < 1) except for one codon at position 92 which was under positive selection. This study suggests that negative selection was most important evolutionary factor driving the genetic evolution of ACLSV.