Intrahost mechanisms governing emergence of resistance-breaking variants of Potato virus Y

The emergence of resistance breaking (RB) variants starting from the avirulent Potato virus Y NN strain (PVYNN) was analyzed after imposing different selective host constraints. Tobacco resistance to PVYNN is conferred by va in both NC745 and VAM genotypes, but VAM carries an extra resistance gene, va2. RB-variants emerged only in NC745 and unexpectedly accumulated higher in the original host, tobacco B21, than the parental PVYNN. However, the recovery of RB-variants was interfered by PVYNN in mixed infections. Further analysis indicated that RB-variants also arose in tobacco VAM, but they were limited to subliminal local infections. Their inability to breakout was associated with absence of a mutational adaptation in the viral VPg gene, which implied a loss of fitness in tobacco B21. Altogether, the emergence of RB-variants was conditioned by inherited host constraints, interference by co-infecting avirulent virus genotypes, and fitness tradeoff of virus adaptations.

► PVY resistance in tobacco VAM is conditioned by two recessive genes.
► The two tobacco recessive genes act at different steps of the infection process.
► Stepwise mutations occur in the emergence of PVY resistance breaking (RB) variants.
► The emergence of RB-variants is interfered by coinfecting avirulent PVY genotypes.
► RB-variants of PVY exhibit loss of fitness in the original susceptible host.