Background and Aims: Although little cherry disease (LChD) is considered as one of the main virus diseases of cherry in several countries, however, to date, there is no data on the incidence of LChV-1 in Iran, the main region of commercial sweet cherry production in West Asia.
Materials and Methods: Sweet cherry orchards in north-west Iran including West Azarbaijan, East Azarbaijan Tehran and Qazvin provinces, were surveyed for Little cherry virus 1 (LChV-1) infection. RT-PCR tests of symptomatic leaf samples, using specific primers for LChV-1 coat protein gene (CP). Using CP sequences the phylogenetic tree was constructed and molecular analysis and population differentiation was indicated by different approaches.
Results: Using specific primers a DNA fragment of the expected size about 500 bp in five out of 43 samples, were amplified. Phylogenetic analysis indicated that the LChV-1 isolates clustered into five groups, which three Iranian isolates fell into GII without a host or geography-based correlation. High nucleotide diversity was determined between the different phylogenetic groups, whereas the within-group diversity of LChV-1 CP gene was evens less. The low nucleotide diversity and high haplotype diversity indicated that the LChV-1 population experienced a bottleneck effect and the population underwent growth after a period of low efficient population size. In addition, the dNS/dS ratios indicate that the GIII is probably under weak positive selection and the GI and GII under strong negative selection. Conclusions: This study showed for the first time the incidence of LChV-1 in sweet cherry orchards in Iran, which is putatively associated with various plant disorders.