Genetic diversity of potato leafroll virus is shaped by variant displacements and selective pressures imposed by aphid and tuber transmission routes

Potato leafroll virus (PLRV) is a major pathogen affecting potatoes worldwide. Since 2018, PLRV incidence increased in Scottish potato crops. Deep sequencing of PLRV in Scottish potato plants revealed the prevalence of a novel PLRV type which became predominant in 2023, displacing the phylogenetically distinct variants that have been present in the region since at least 1989. Analysis of the infection dynamics of the cDNA clone-derived PLRV isolates in potato plants indicated that the novel PLRV may accumulate to higher levels compared to the historic one. Analysis of the genetic diversity of PLRV in early and late field generations (FGs) of seed potatoes showed a significantly reduced genetic diversity of the PLRV structural genes in the early FGs, compared to the late FGs, while divergency of the non-structural genes remained similar across all FGs. Considering that late FGs are more likely to be infected with PLRV via tuber transmission, and early FGs via aphid transmission, these findings suggest that aphid transmission imposes a genetic bottleneck on the structural genes of PLRV, but not on its non-structural genes.