Low genetic diversity of a natural population of Garlic virus D from Poland

Thirty Garlic virus D isolates collected on a local scale over a 2-year period were analysed and compared to others available in GenBank. In total, 1139 nt were sequenced for each isolate, representing about 13 % of the complete virus genome. Bioinformatic analysis revealed that despite the wide geographic distribution and different growing conditions of hosts, GarV-D maintains an amino acid similarity between 95 to 100 % and 88 to 100 %, indicating high spatial and temporal genetic stability of the coat protein (CP) and nucleic acid binding protein (NABP) genes. The sequence alignments of all isolates of GarV-D were also searched for evidence of recombination and diversifying selection. The ratio of non-synonymous to synonymous polymorphic sites indicated that mostly purifying selection has acted within the analysed genes. However, three codons (two in CP and one in NABP sequences) showed to be under positive selection, including codon located inside conserved zinc-motif finger.