Identification of Two Novel Recombinant Types of Potato Virus Y from Solanum tuberosum Plants in the Southern Region of Russia

Potato virus Y (PVY; genus Potyvirus, family Potyviridae) is one of the most devastating and economically important potato pathogens. Members of the Potyviridae family demonstrate high recombination rates. In nature, five major parental variants of PVY were identified with at least 35 recombinants. In this study, we report two novel PVY recombinants discovered in the sprouts of potato tubers produced in field conditions in the Astrakhan region of Russia in 2021 using high-throughput sequencing and de novo genome assembly. These recombinants, which were named Ast-A-I and Ast-A-II, have previously unknown arrangements of genome sections derived from PVYO and PVYN, with a novel recombination junction at position 7,850 nt of the PVY genome in the middle part of the RNA-dependent RNA polymerase (NIb) gene, with PVYO type sequence at the 5¢ end relative to this junction and PVYN type at the 3¢ end. Other recombinant junctions in the novel PVY variants were previously found in PVYNTNa and PVYNTNb. This includes those at positions 2,390 and 9,200 (PVYN at the 5¢ end and PVYIS° at the 3¢ end), which were present in both novel recombinants, and at position 500 (PVYO at the 5¢ end and PVYN at the 3¢ end), which present in Ast-A-II. The presence of PVY variants with a novel recombinant point is verified by Sanger sequencing. Phylogenetic analysis of genomic RNA showed that the sequences of these recombinants form a separate branch that do not cluster with previously described PVY strains.