First Report of Potato yellowing virus (Genus Ilarvirus) in Solanum phureja from Ecuador

Abstract

A bacilliform virus, named Potato yellowing virus (PYV), causing chlorosis of leaves was reported in 1992 in potato (Solanum tuberosum) fields in Peru (1) and symptomless wild potatoes (S. fernandezianum) in Chile (4). PYV is reported as an alfamo-like virus (1) (family Bromoviridae) but no sequence information is available for this virus, making its taxonomic position inside the Bromoviridae uncertain (currently this family is organized into five genera: Alfamovirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus). Herein we report the presence of PYV in native potatoes (Solanum phureja) collected from Ecuador where the crop constitutes an important source of income in rural communities. Forty accessions of S. phureja collected in Ecuador in June 1986 and maintained in vitro at the International Potato Center (CIP) germplasm bank were analyzed by double-antibody sandwich (DAS)-ELISA with antiserum raised against a Peruvian isolate of PYV (1). PYV was detected in six accessions (15% of the material) corresponding to cultivars Chaucha Tomate and Chaucha Blanca (from the province of Cañar), Chaucha Negra Ojona and Chaucha Amarilla (Loja Province), and Cuica and Chaucha (Azuay Province). Mechanical inoculation of the indicator plant Physalis floridiana with leaf extracts of these six plants, a PYV isolate from Peru (1) (positive control), and an additional four plants testing negative for PYV (negative controls) induced symptoms of mosaic and leaf deformation only with the six clones from Ecuador and the PYV isolate from Peru. To further confirm the presence of the virus, we used universal PCR primers designed for the Bromoviridae (Ilar1F5: 5′-GCNGGWTGYGGDAARWCNAC-3′ and Ilar1R7: 5′-AMDGGWAYYTGYTYNGTRTCACC-3′) that target the helicase motif (RNA1) (3). Total RNA was extracted from 200 mg of leaf material (from potato and mechanically inoculated P. floridiana) using Trizol (Invitrogen, Carlsbad, CA) following the manufacturer's instructions and cDNA was synthesized using random hexamer primers. We obtained a reverse transcription-PCR amplified band only from samples that were DAS-ELISA positive to PYV. To identify the virus at the genus level, we cloned the PCR fragments (265 nucleotides) from four of the samples from Ecuador and the Peruvian isolate into plasmid vectors (pGEM-T Easy Vector cloning system; Promega, Madison, WI) for Sanger sequencing (Macrogen, Seoul, Korea). Phylogenetic analysis grouped PYV sequences with those of the genus Ilarvirus. Among the ilarviruses, Fragaria chiloensis latent virus (2) was the closest relative of PYV, with which it shares 77% nucleotide and 85% amino acid sequence identity. PYV isolates from Ecuador split into two different variants (91% identity) that shared 93% nucleotide and 99% amino acid sequence identity with the Peruvian isolate. Collectively, the data suggest that PYV is a distinct ilarvirus and that it is more widely spread among South American potatoes than previously suggested. The GenBank Accession Numbers for the sequences described are: HQ141053 (Loja1), HQ141054 (Azuay), HQ141055 (Cañar), and HQ141056 (Loja2) for the isolates from Ecuador and HQ141057 (PYV-Cañete) for the isolate from Peru. References: (1) S. Fuentes and U. Jayasinghe. Fitopatología 28:22, 1993. (2) I. E. Tzanetakis and R. R. Martin. Virus Res. 112:32, 2005. (3) M. Untiveros et al. J. Virol. Methods 165:97, 2010. (4) J. P. T. Valkonen et al. Potato Res. 35:411, 1992.

Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences

“…The virus was later renamed potato yellowing virus [29, 30, 31]. In subsequent studies, PYV was reported on potato and pepper plants from Chile and Ecuador with only partial sequence information provided [32, 33] covering less than 1 kb of the genome. Our PYV isolate (PV-0706) was obtained from a pepino fruit ( Solanum muricatum ) of unknown geographic origin purchased in a German supermarket and was propagated on D .…”

Development and application of a universal and simplified multiplex RT-PCR assay to detect five potato viruses

“…phureja in Ecuador (Silvestre et al 2011). The first complete PYV genome sequence was obtained in 2019 using HTS of sequences enriched by immunocapture of virions (Knierim et al 2019).…”

Occurrence of potato yellowing virus in naranjilla (Solanum quitoense Lam.) in Ecuador

“…The RNA dependent RNA polymerase gene (RdRp) was used for a phylogenetic analysis using BEAST under the LG+G model and a strict molecular clock. The phylogeny showed that the PYV isolate from naranjilla clustered with an isolate described in pepper from the same location in Tumbaco (KP772263) (Sivaprasad et al 2015), but was distantly related with isolates from Solanum phureja from other locations in Ecuador (Silvestre et al 2011) Moreover, the PYV RNAs have 80.1, 78.1 and 73.5 identity with Fragaria chiloensis latent virus, (NC_006566, NC_006567, NC_006568) which confirms that PYV as a distinct Ilavirus (family Bromoviridae). To our knowledge, this is the first report of PYV infecting S. quitoense as a new host.…”