Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences

Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVSᴼ) or Andean (PVSᴬ) strains. Five isolates – 41956, Cosimar, Galaxy, ND2492-2R, and Q1 – were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa, whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVSᴼ. PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVSᴼ, while Q3 and Q5 clustered with known PVSᴬ strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVSᴬ and PVSᴼ strains, a higher π value was found for PVSᴬ. Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVSᴼ, whereas a balancing selection pressure was found on PVSᴬ.