Phylogenetic analysis of Iranian Apple Stem Grooving Virus Isolates Using Coat Protein Gene

Apple stem grooving virus (ASGV) is one of the economically important latent viruses infecting pome fruit trees worldwide. The investigation on the distribution of ASGV and its molecular properties can give us more information about the epidemiology and control of this latent and graft-transmissible virus.

The presence of ASGV in apple and pear orchards in Mazandaran province (Northern Iran) was investigated using serological and molecular approaches. The phylogenetic tree was constructed by the Neighbor-Joining method implemented in MEGAX. Two-dimensional nucleotide diversity plot constructed using CP sequences by SDTv1.2 version 12. RDP4 and Dnasp software were used for recombination, and genetic diversity and demographic analysis, respectively v. 6.10.04.

ASGV was detected in 10.2% of leaf samples by ELISA test. A DNA amplicon with the expected size of 780 bp corresponding to the ASGV coat protein (CP) gene was amplified using RT-PCR assay. Phylogenetic analysis showed that the ASGV isolates clustered into two main groups, which is confirmed by the nucleotide identity plot. Group II (GII) includes two Chinese and Korean pear isolates with an apple isolate from India. However, most of the ASGV isolated from different geographical regions including Iranian isolates fell into group I (GI). High nucleotide identity (91 to 100%), low nucleotide, and high haplotype diversities indicate the recent distribution of ASGV. No clustering was found according to the hosts or where the ASGV was isolated. Using dN/dS values it was found that the different populations of ASGV are under negative (purifying) selection with the ω ratio less than 1. The highest gene flow was determined between American and South Asian populations. Moderate or low genetic differentiation, and frequent gene flow (FST < 0.33 and Nm > 1) also confirmed with Ks*, Kst* Z, Z* and Snn statistics values, except between West Asia and East Asia populations which may suggesting these isolates are older than the others. 

To our knowledge, this is the first report of ASGV infecting apple and pear trees in North Iran, which extends the geographical range of this viral disease. Accordingly, larger-scale ASGV investigations must be conducted to determine the distribution and prevalence of this virus in Iran.