Phylogrouping and pathogrouping of Potato virus Y isolates from pepper plants in Turkey

Abstract Potato virus Y (PVY) causes yield loss of pepper (Capsicum) crops worldwide, but little is known of its molecular diversity in pepper in Turkey or elsewhere. During 2016 and 2017, pepper crops were surveyed in three different provinces of Turkey, and plants with virus-like symptoms were collected. Four hundred and twenty one samples were collected and 35 found to be infected with PVY by DAS-ELISA using PVY-specific antisera. The positive samples were tested by RT-PCR and viral genes of some were sequenced. Conventional comparisons indicated that eight of the isolates were probably from phylogroup C, and three from pathogroup N-Wi, which is part of phylogroup R1. Other methods of using sequence data were tested in an attempt to identify how PVY, a multiply recombinant virus, can be most economically phylogrouped; one using Genbank searches and a database of over 600 PVY complete genomic ORF sequences was found to be effective and objective. The same data confirmed that sequencing the P1 and CP genes is more cost effective for phylogrouping PVY than other gene combinations. This is the first report of recombinant PVY isolates in pepper plants in Turkey.