Molecular Characterization of Potato virus V (PVV) Infecting Solanum phureja Using Next-Generation Sequencing

Abstract

Viral diseases are one of the most limiting problems in the production of potato worldwide. Solanum phureja constitutes one of the most susceptible materials to viral diseases in Colombia; however, there are few studies on viruses infecting this crop. In the current study, we performed a molecular characterization of Potato virus V (PVV) that infects S. phureja, using different potato plots located in the province of Antioquia, using Next-Generation Sequencing (NGS), DAS-ELISA, real time RT-PCR (RT-qPCR) and RT-PCR. Results revealed variable levels of incidence among plots (6.7 %-86 %) and the presence of two slightly different variants (Var_A and Var_B) present in approximately 72 %:28 % ratio. These PVV strains have a genome of 9828 nt codifying for a polyprotein of 3066 aa and share high nucleotide sequence identity (99,7 % in their complete genome) with respect to PVV-Phureja, recently described in Colombia, but are very divergent with respect to currently available PVV genomes (82-83 %). The genome information was used to design two sets of primers, useful in the specific detection of this virus in S. phureja leaf samples through RT-PCR (459 bp) and RT-qPCR (89 bp, Ct=12.08-21.86; Tm=78.7 °C-80.2 °C). This study underscores the importance of including diagnostics of PVV in S. phureja tuber-seed certification programs in Colombia.

Keywords

• DAS-ELISA
• NGS
• papa
• Potyvirus
• RT-qPCR