Turkish isolates of alfalfa mosaic virus belong to a distinct lineage among global population

Complete RNA3 sequences of 15 alfalfa mosaic virus (AMV) isolates sampled from Afyonkarahisar, Ankara, Konya, Tokat, Kayseri, and Nevşehir Provinces of Türkiye were obtained using RT-PCR with two primer pairs designed in this study. Molecular and population analyses were performed on them together with 63 global isolates which full genome sequences available in NCBI GenBank. Phylogenetic analysis based on movement protein (MP) and coat protein (CP) regions showed unrelated isolates clustering between the constructed trees, and the new Turkish isolates were dispersed in different phylogroups. Particularly, three new Turkish potato isolates: B6, K1, and K2 occupied a divergent MP lineage, together with one alfalfa isolate from China: ZM1 NX3. S, η, and k parameters of genetic diversity confirmed that CP were more conserved than MP sequences. The 15 new Turkish isolates shared 95.4–100% nucleotide and 94–100% amino acid, and 92.8–100% nucleotide and 93.3–100% amino acid identities among themselves at MP and CP regions, respectively. All tested populations were found to be under very strict purifying constraints (dN/dS ratios of 0.061–0.219), and had undergone recent expansion, probably due to new mutations in their genome, according to diversity and neutrality tests. Fixation index (FST) values obtained by pairwise comparisons of phylogroups were all above 0.33, suggested that the isolates clustering has been done convincingly.