Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications

In 2020, 264 samples were collected from potato fields in the Turkish provinces of Bolu, Afyon, Kayseri and Niğde. RT-PCR tests, with primers which amplified its coat protein (CP), detected potato virus S (PVS) in 35 samples. Complete CP sequences were obtained from 14 samples. Phylogenetic analysis using non-recombinant sequences of (i) the 14 CP’s, another 8 from Tokat province and 73 others from GenBank; and (ii) 130 complete ORF, RdRp and TGB sequences from GenBank, found that they fitted within phylogroups, PVS(I), PVS(II) or PVS(III). All Turkish CP sequences were in PVS(I), clustering within five subclades. Subclades 1 and 4 were in three to four provinces, whereas 2, 3 and 5 were in one province each. All four genome regions were under strong negative selection constraints (ω = 0.0603–0.1825). Considerable genetic variation existed amongst PVS(I) and PVS(II) isolates. Three neutrality test methods showed PVS(III) remained balanced whilst PVS(I) and PVS(II) underwent population expansion. The high fixation index values assigned to all PVS(I), PVS(II) and PVS(III) comparisons supported subdivision into three phylogroups. As it spreads more readily by aphid and contact transmission, and may elicit more severe symptoms in potato, PVS(II) spread constitutes a biosecurity threat for countries still free from it.