Variability and population structure of watermelon mosaic virus in zucchini crops in Poland

Watermelon mosaic virus (species Potyvirus citrulli, WMV) poses a significant threat to various cucurbit species worldwide. In Poland, the virus has been consistently recorded in Cucurbita pepo var. giromontiina crops since 2008. To analyse the genetic diversity and population structure of WMV in Poland, comprehensive surveys were conducted in two major agricultural regions, Greater Poland and Kuyavian-Pomeranian Voivodeships (west-central and mid-northern regions of Poland, respectively). To better understand the WMV occurrence, over 1,800 leaf samples were randomly collected from symptomatic and asymptomatic zucchini and weed plants. Moreover, aphids were also analysed for the presence of the virus. In this study, 154 complete coat protein gene sequences of WMV isolates collected between 2013 and 2024 were obtained using Sanger or high-throughput sequencing. The sequence identity of the Polish WMV isolates ranged from 92.8 to 100% and 95.4 to 100% for nucleotide and amino acid sequences, respectively. Unique mutations were identified in the isolates originating from the Kuyavian-Pomeranian region. Moreover, a novel KEET motif was identified in nine isolates, which has not been reported in previous studies. Most CP codons undergo negative selection; however, eight positively selected sites were detected. Phylogenetic analysis revealed that the Polish isolates were grouped in both classical and emergent main phylogenetic clades. The population analyses indicated limited or no gene flow between WMV subpopulations, suggesting that genetic drift may be considered an important evolutionary force shaping the viral diversity.