Welcome to the University of Idaho's Potyvirus database. With this tool you may search Potato Virus Y strains by phenotype, location and/or collection date. You may then view and compare viral nucleotide and protein sequences, and download aligned or unaligned protein or nucleotide sequences.

Potato virus is re-emerging as a serious and an immediate threat for the U.S. potato industry. Recent studies have identified an explosion of genetic and biological diversity in the PVY population leading to a widespread distribution of damaging necrotic variants that were recently considered to be absent in North America. Nevertheless, the population structure, recombination potential, and pathogenicity of PVY strains in different environments and in prominent potato varieties remain poorly understood. This project seeks to fill the existing knowledge gap by characterizing the entire PVY complex and correlating sequence data with various biological phenotypes. Two of the co-PIs were the coordinators and principle scientists for a 3-year (2004-07) survey of PVY diversity in U.S. and Canadian seed potato production areas. More that 2,500 PVY isolates were analyzed by multiplex RT-PCR to determine their strain identity (Lorenzen et al 2006) as well as tested for their reaction against a panel of strain-specific monoclonal antibodies and their ability to induce necrosis in tobacco. Additionally we have access to a similar size collection from Canada and we have a growing list of collaborators providing us with PVY isolates from Central and South America. This project will directly result in new methods to detect and differentiate various novel PVY strains, and will be invaluable for potato breeding program focused on PVY resistance.

This project is funded by a grant from the U.S. Department of Agriculture through the CSREES (Award No. 2009-35600-05025). The website and computational facilities are supported by grants from the National Institutes of Health/National Center for Research Resources (P20RR016454 and P20RR16448).

About PVY

Potato virus Y (PVY) is a type member of the genus Potyvirus in the family Potyviridae, which is the largest plant virus family (Berger et al., 2000). PVY, like other potyviruses, is transmitted from plant to plant either mechanically (through wounds) or by aphids. In vegetatively propagated crops, like potato, transmission via vegetative material, i.e. seed tubers, is of major importance. PVY belongs to a superfamily of picorna-like viruses (Koonin and Dolja, 1993), which includes several evolutionarily related plant viruses with similar genome expression strategies, e.g. family Comoviridae, and a large group of animal viruses currently compiled in the order Picornavirales. The ca. 9.7-kb, positive-strand RNA genome of PVY carries a VPg-protein, covalently linked to the 5′-terminus, and a poly(A)-tail at the 3′-end. The genome of PVY, like other potyviruses, is expressed through successive processing of a single, ca. 300-kDa polyprotein into 10 proteins by three virus-encoded proteases. In nature, PVY exists as a complex of multiple strains or isolates with different pathologies on different crops. PVY is an important pathogen for cultivated solanaceous crops, like potato, pepper, tomato, and tobacco. But by far PVY is the most important pathogen for potato. Based on symptomatology in tobacco, two main groups of PVY strains were defined (e.g. Kerlan, 2006): O-strains generally cause mild symptoms, like vein clearing, mild mosaic, and mild growth delay; N-strains cause vein necrosis, stunting, and leaf deformations. Worldwide distribution of these two types of PVY is uneven, and tends to change. Specifically, O-strains of PVY (PVYO) have been present in North America for a long time, while N-strains (PVYN) appeared in the field in 1990 (Singh, 1992). Since the early 1990s, N-strains have been found in Canada and in the U.S. Three additional PVY strain groups were identified, based on pathology in potato carrying different resistance genes, i.e. PVYC, PVYZ, and PVYE. Current nomenclature of the PVY strains has recently been discussed and updated (Singh et al., 2008), we use it throughout this website.

Serotype Information

For many of the samples, serological phenotype has been determined by TAS-ELISA using three monoclonal antibodies. Monoclonal antibody 4C3 reacts with PVY isolates belonging to all strains, 1F5 is specific to PVYN and PVYNTN, and MAb2 is specific to the PVYO, PVYN:O, PVYN-Wi, and PVYC strains. For some samples, serological phenotype has been determined by Western blots using PVYN specific monoclonal antibody SASA-N.

Serotype strain vs. monoclonal antibody.
O + - + - +
C + - + - +
N + + - + -
NTN + + - + -
N:O + - + - +
O5 + + + - +

RT-PCR information

Separation of PCR products for the PVY strain types and from mixed cultures
(Lorenzen, et al. 2006)

Isolates were characterized by multiplex reverse transcription PCR, which can assign isolates to the major PVY strain types.

Phenotype Information

Click for larger image
Hu et al. 2009a

Typical reactions in the plant due to the virus are necrosis in tobacco leaves, and Potato Tuber Necrotic Ringspot Disease (PTNRD). It should be noted that different strains present differently in different tubers. In some cases, PTNRD only presents in about 20% of all infections.

(A) Symptoms induced by L26 in tobacco (cv. Burley) 3 weeks post-infection. Symptoms induced by reference isolates Oz (PVYO) and 423-3 (PVYNTN) are also shown.
(B) Tuber symptoms in potato cv. Yukon Gold induced by several PVY isolates which belong to the common strain, PVYO pathotype (Oz), or to the necrotic strain, PVYNTN pathotype (PB312, N4, HR1, and L26).


Berger, P.H., Barnett, W.O., Brunt, A.A., Colinet, D., Edwardson, J.R., Hammond, J., Hill, J.H., Jordan, R.L., Kashiwazaki, S., Makkouk, K., Morales, F.J., Rybicki, E., Spence, N., Ohki, S.T., Uyeda, I., van Zaayen, A., and Vetten, H.J. 2000. Family Potyviridae. In: Virus Taxonomy. 7th Teport of the International Committee on Taxonomy of Viruses (van Regenmortel et al., eds). Academic Press: San Diego, CA; pp. 703-724.

Hu, X., A. V. Karasev, C. J. Brown, J. H. Lorenzen. 2009. Sequence characteristics of potato virus Y recombinants. Journal of General Virology. doi: 0.1099/vir.0.014142-0

Hu, X., T. Meacham, L. Ewing, S. M. Gray, A. V. Karasev. 2009a. A Novel recombination Strain of Potato Virus Y suggests a new viral genetic determinant of vein necrosis in Tobacco. Virus Res. 143:68-76.

Lorenzen, J.H., L.M, Piche, N.C. Gudmestad, T. Meacham, P. Shiel, 2006. A multiplex PCR assay to characterize Potato virus Y isolates and identify strain mixtures. Plant Disease 90:935–940.

Karasev, Alexander V., Xiaojun Hu, Celeste J. Brown, Camille Kerlan, Olga V. Nikolaeva, James M. Crosslin, Stewart M Gray. 2011. Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101:778-785.

Kerlan, C. Potato virus Y. 2006. Descriptions of Plant Viruses, No. 414. Association of Applied Biologists.

Koonin, E.V. and Dolja, V.V. 1993. Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. Crit. Rev. Biochem. Mol. Biol. 28: 375-430.

Singh, R. P. 1992. Incidence of the tobacco veinal necrotic strain of Potato virus Y (PVYN) in Canada in 1990 and 1991 and scientific basis for eradication of the disease. Can. Plant Dis. Surv. 72:113-119.

Singh, R. P., J. P. T. Valkonen, S. M. Gray, N. Boonham, R. A. C. Jones, C. Kerlan, J. Schubert. 2008. Discussion paper: The naming of Potato virus Y strains infecting potato. Arch. Virol. 153:1–13