1

Canada/US-Management Plan for Potato 

Viruses that Cause Tuber Necrosis 

October 25, 2004

U.S. Department of Agriculture 

Animal and Plant Health Inspection Service 

Plant Protection and Quarantine 

4700 River Road, Unit 140 

Riverdale, MD 20737 

Canadian Food Inspection Agency 

Plant Protection Division 

59 Camelot Drive 

Ottawa, Ontario 

K1A 0Y9 
2

TABLE OF CONTENTS 

1. Introduction and Goals.............................................................. 3 

2. Definitions and Descriptions....................................................... 3 

3. Virus Management Methods....................................................... 6 

3.1 PVY Complex.......................................................................... 6 

3.2 Potato Mop Top Virus................................................................ 7 

3.3 Tobacco Rattle Virus.................................................................. 7 

3.4 Alfalfa Mosaic Virus....................................................................8 

3.5 Shipping Point Inspection ............................................................ 8 

4. Scoping survey for PVY Complex ................................................. 9 

5. Research Needs........................................................................ 9 

6. Training needs ........................................................................ 10 

7. Implementation ....................................................................... 10 

8. Revision ................................................................................. 10 

9. Endorsement ........................................................................... 10 

10. References ............................................................................ 11 

Appendices ............................................................................... 12 

 

Appendix 1 - North American PVY Strain Survey – Crop Year 2004 
3

1. Introduction and Goals 

The Canadian Food Inspection Agency (CFIA) and the U. S. Department of Agriculture 

Animal and Plant Health Inspection Service (APHIS) announced, on December 23, 2002, 

that a joint potato virus management plan will be developed to maintain high quality seed 

potato production. 

This plan proposes immediate measures to manage the risks associated with several pests 

that occur in both countries, including Potato mop top virus (PMTV), Potato virus Y 

(PVY) complex and Tobacco rattle virus (TRV), through seed potato certification 

measures. Through surveys and research, data will be collected and evaluated to better 

understand the biology of these viruses and their vectors, thus enabling the establishment 

of further control measures. 

CFIA and APHIS are working cooperatively to protect each country's agricultural and 

environmental resources and agree to take actions that are least disruptive to trade. 

CFIA and APHIS also agree to work collaboratively with respective seed potato 

certification agencies and potato organizations to harmonize and make transparent, seed 

certification procedures to control viruses causing internal tuber necrosis. Successful 

management of viruses that cause internal tuber defects and their respective vectors will 

contribute to maintaining high seed potato phytosanitary quality and minimize impacts on 

commercial potato production. 

This plan replaces the previous PVYN management plan dated March 2, 1994 and 

amended October 5, 2001. The objective of this plan remains to facilitate trade of 

potatoes within and between Canada and the USA, while minimizing the impact on the 

tobacco industry caused by the tobacco-necrotic isolates of PVY infecting the potato 

crop. Additionally this plan has the objective to manage the incidence of PMTV and 

TRV and minimize the impact of these viruses on US and Canadian potato industries. 

2. Definitions and Descriptions 

Crop: 

A variety and class of seed potatoes, growing in an aseptic environment, a protected 

environment or in one or more fields of a farm unit.* 

Farm Unit: 

a. A single tract of land, operated for the production and marketing of seed potatoes 

under the control of one grower, or 

b. A number of separate tracts of land, operated as a single unit, with the use of common 

equipment, facilities or storage, for the production and marketing of seed potatoes under 

the control of one grower. 

Field: 
4

Identifiable area of land on which seed potatoes of a particular variety and class are 

planted or have been produced. 

Flush-Through Production System: 

System of seed potato production in which material is allowed to remain in the system for 

a limited number of generations. 

Inspection: 

Official visual examination of plants, plant products or other regulated articles to 

determine if pests are present and/or to determine compliance with phytosanitary 

regulations.* This includes visual examination as part of a federally recognized quality 

assurance program. 

Lot: 

A population of certified seed potatoes of one variety and class that is identified by one 

certificate number. 

Nuclear material: 

Plant material produced in an aseptic or protected environment. 

Positive Lot, Crop or Field: 

A lot, crop or field, where the presence of a pathogen has been confirmed, based on 

recognized tests. 

PVY Complex: 

Potato virus Y (PVY) is the type-species of the Potyvirus genus. It is a positive strand 

monopartite RNA virus that infects primarily solanaceous plants including potato, 

tomato, tobacco, and pepper. PVY occurs as a complex of virus strains that can be 

distinguished by reactions on tobacco and potato cultivars. Recognized strains covered 

by this plan include, but are not limited to: 
5

Strain Group Symptoms Other Distinguishing 

Characteristics 

PVYO Mosaic, leaf and stemnecrosis, leaf drop or veinal 

necrosis in potato 

Mosaic in tobacco, mild to 

severe mosaic in potato; 

hyper sensitive response in 

potato with Ny and Nc 

genes 

PVYN Mosaic or mild mosaic in 

potato, veinal necrosis in 

tobacco 

Serologically 

distinguishable from 

PVYO/C; coat protein 

sequence phylogenetically 

distinct from PVYO/C

PVYNTN

note: may include several 

distinct isolates/groups 

Mosaic or veinal necrosis in 

tobacco, necrotic arcs and 

ring spots in tubers of some 

potato cultivars 

Serologically 

distinguishable from 

PVYO/C; coat protein 

sequence phylogenetically 

distinct from PVYO/C

PVYN:O Symptoms may vary. Some strains are not 

serologically or 

phylogenetically distinct 

from PVYO/C

Quality Assurance System: A planned and regularly monitored framework of controls, 

based on documented procedures, which is applied to critical operational activities in the 

production of potatoes or the performance of a service (e.g. diagnostics) or activity (e.g. 

conducting a test) to ensure operational efficiency and reliable compliance with specified 

quality standards. (NAPPO RSPM 3, 2002)

Shipping Point Inspection: 

Inspection of seed potatoes shortly before or at time of shipment to determine the product 

complies with seed potato grade standards recognized by the US and Canada seed potato 

regulatory agencies.

Test: 

Official examination, other than visual, to determine if pests are present or to identify 

pests*. 

Tuber Necrosis: 

Necrotic dark brown arcs, rings and/or flecks in the tuber tissue often associated with 

necrotic rings on the tuber surface. Tuber necrosis is also referred to as spraing 

depending on the virus. 

* FAO Glossary of Phytosanitary Terms, 2002 
6

3. Virus Management Methods 

3.1 Potato Virus Y (PVY) Complex 

3.1.1 Nuclear Material 

 In-vitro material 

 All plants in a tissue culture bank must be tested and found free of PVY. 

 Any material introduced into tissue culture must be tested and found free of PVY. 

 Any tissue culture material testing positive for PVY cannot be used to produce 

certified seed potatoes, unless the virus is eliminated. 

 Protected Environment (greenhouse / screenhouse/growth chamber) 

Certification rules concerning production in protected environment must include the 

following 

 Seed potato production in a protected environment will be tested at least annually 

for PVY at a target rate of 1% of the plants, with a minimum of 5 plants per 

crop/lot. It is recommended that testing takes place every crop cycle. 

 Any crop/lot grown in a protected environment that tests positive for PVY must 

be destroyed, unless it is found to be PVYO alone, in which case it can be 

downgraded. 

 If aphid vectors are detected in the protected environment, when the crop is 

growing, testing must be conducted to determine freedom from PVY. 

3.1.2 Field Grown Seed 

 Inspection for PVY complex symptoms will be included in seed certification 

agencies’ inspection procedures. 

 A sample of suspect plants observed during field inspection will be tested to 

determine if the symptoms are caused by PVY. : If PVY presence is confirmed 

the tolerances for mosaic must be enforced. 

 

3.1.3 Field Generation 2 

All Field Generation 2 (FG2) material will be sampled and tested for the presence of 

PVY and PVYN. A total of 400 leaves will be collected and tested from up to 10 seed 

lots/crops per farm unit. The collection of the 400 leaves will be proportional and 

random across the crops or lots to be tested. 

 Tolerances of the state and federal certification programs apply.

 If a farm unit has less than 10 FG2 crops/lots the sample size for the farm will still 

be 400 leaves. 
7

 If the farm unit has more than 10 FG2 crops/lots an additional sample of 400 

leaves will be submitted for testing from every group of 10 lots or less. 

 If crops/lots are found positive for PVYN, all FG2 crops/lots on that farm, and 

lots/crops that are progeny of the same seed lot as the positive crops/lots, must be 

sampled and tested at a rate of 400 leaves per lot. 

 Regulatory action will only be taken on FG2 crops/lots. PVYN positive crops/lots 

of FG2 can only be used for the production of commercial crops, not for 

recertification.

The testing of FG2 crops/lots may be done either during the growing season or post 

harvest. If done post-harvest, leaves from grown-out plants or sprouts from tubers must 

be used. 

 Leaf testing will be done by ELISA using an appropriate protocol. An ELISA 

positive for PVYN will be considered a suspect positive. Confirmatory tests must 

be conducted with PCR and/or bioassays. 

3.2 Potato Mop Top Virus (PMTV) 

3.2.1 Nuclear Material 

 All plants in a tissue culture bank must be tested and found free of PMTV. 

 Any material introduced into tissue culture must be tested and found free of 

PMTV. 

 Any tissue culture material testing positive for PMTV cannot be used to produce 

certified seed potatoes, unless the virus is eliminated. 

3.2.2 Field Grown Seed 

 Inspection for PMTV related symptoms will be included in seed certification 

agencies’ inspection procedures. Training material on PMTV symptoms in plants 

will be provided to all field inspectors. 

 Plants symptomatic for PMTV must be eliminated before final inspection. 

 PMTV will also be regulated through the inspection of seed shipments. 

3.3 Tobacco Rattle Virus (TRV) 

3.3.1 Field Grown Seed 

 Inspection for TRV related symptoms will be included in seed certification 

agencies’ inspection procedures. Training material on TRV symptoms in plants 

will be provided to all field inspectors. 

 Plants symptomatic for TRV must be eliminated before final inspection. 
8

 TRV will also be regulated through the inspection of seed shipments. 

 

3.4 Alfalfa Mosaic Virus (AMV) 

 Tubers exhibiting necrosis caused by AMV will be scored as an internal defect 

and be allowed for recertification providing the tolerance of 2.0% for internal 

necrosis is not exceeded. 

3.5 Shipping Point Inspection 

3.5.1 Seed for Commercial Production 

 All seed shipments moving from a production State or Canada for commercial 

production must be inspected by federally recognized inspectors or a federally 

authorized cooperator from a facility under a quality assurance system and must 

meet the tolerances for internal necrosis of Table 1 below. If a lot exceeds this 

tolerance, the grower will have the option to re-grade the lot or remove it from the 

seed certification system. 

3.5.2 Seed for Recertification 

 All seed shipments moving from a production State or Canada for recertification 

must be inspected by a federal, state or provincial inspector for tuber necrosis. If a 

lot exceeds the tolerance of 0.5% necrosis caused by PVY complex, PMTV or 

TRV (see Table 1 below), it is not eligible for recertification but may be shipped 

for commercial purposes. 

Table 1: Eligibility of Seed potatoes related to the Percentage of Internal Tuber 

Necrosis, apparently caused by PVY complex, PMTV or TRV 

Percentage Internal Tuber 

Necrosis Scored* 

Seed intended for 

Recertification 

Seed intended for 

Commercial Production 

Less than or equal to 0.5% Eligible Eligible 

Between 0.5 and 2.0% Eligible if negative lab test 

for PVYN/NTN, PMTV, 

TRV 

Eligible 

More than 2.0% Not eligible Not eligible 

Notes: 

 * Internal tuber necrosis will be calculated as percent incidence {(number of tubers 

with internal necrosis/number of tubers sampled) x100}. 

 
9

4. Scoping Survey for PVY Complex

A multi year scoping survey, starting with the 2004 crop will be conducted, coordinated 

by APHIS and CFIA, in each state and province, where seed potatoes are certified. The 

seed lots of the oldest classes in production will be surveyed to determine the incidence 

and makeup of any PVY complex at that point in the seed potato production system. The 

data will be kept confidential and be reviewed annually on a country-wide basis. The 

data will be used confidentially to help determine if the FG2 management protocol is 

effectively managing virus levels of PVY complex. No regulatory action will be taken 

on lots found to be positive in this survey. PVY certification requirements will not be 

changed without proper notification. See Appendix 1 for details of the survey and testing 

protocols. 

5. Research Needs 

Both parties acknowledge the need for and value of multiple virus testing protocols. 

Such protocols should be encouraged as a research goal and new protocols incorporated 

into the plan when available. 

PVY complex 

 Research on the susceptibility of US and Canadian potato varieties to PVYN/NTN. 

 Research on recombinants between PVYO and PVYN to develop appropriate tests 

for these and any other PVYN isolates. 

 Research on the population dynamics and prevalence of recombinant strains to 

determine if changes in the population of strains are occurring. 

 Research on environmental factors that influence symptom expression to develop 

a better understanding of PVY strain symptoms. 

PMTV 

 Research on susceptibility to PMTV to determine if the pathogen causes an 

economic impact on US and Canadian potato varieties. If any varieties are shown 

to be extremely sensitive to PMTV, a specific management plan for those 

varieties should be developed. 

 Research on the control of powdery scab since control of the vector will lead to 

control of PMTV. 

 Research on improved testing methodologies for PMTV to improve the detection 

of the pathogen. 

TRV 
10

 Research on improved testing methodologies for TRV to improve the detection of 

the pathogen. 

 Research on the control of the TRV vector since control of the vector will lead to 

control of TRV. 

 Research on the efficiency of the nematode vector to acquire the virus from 

infected potato plants to determine a better understanding of the dynamics of the 

vector/virus interaction. 

6. Training needs 

 Inspectors involved in shipping point and field inspection of seed potatoes will be 

trained annually by state, federal, provincial and/or university officials on 

symptoms of PVYN/NTN, PMTV and TRV in tubers and plants to assist them in 

their inspection efforts. 

 APHIS and CFIA will develop a manual to differentiate spraing symptoms from 

other causes of internal necrosis. 

 An appendix of pest management practices for controlling viruses addressed in 

this plan and their vectors will be added upon completion. 

7. Implementation 

 

 It is essential that APHIS and CFIA participate in the implementation of this plan, 

and oversee the application of all of its elements. Seed potatoes produced and 

certified by a federal or state certification agency must comply fully with the 

content of the management plan. 

 It is understood that some elements of the management plan will require 

amendments to regulations, rules, policies and inspection manuals. Therefore, 

every certification agency, including CFIA and APHIS, must make the necessary 

amendments to achieve full implementation of the plan within 12 months from the 

date of signature. 

8. Revision 

 This plan will be reviewed after three years by APHIS and CFIA or as needed at 

the request of either party. Results of all reviews and any recommended 

modifications to this plan will be shared with federal, state and provincial 

regulatory officials, the potato industry and the tobacco industry for comment.

, 

9. Endorsement 

The Canadian Food Inspection Agency and the United States Department of 

Agriculture Animal and Plant Health Inspection Service agree to full 

implementation of this management plan with an ultimate goal of using existing 

seed certification programs to control viruses that cause tuber necrosis. 
11

CFIA USDA APHIS 

Date: Date: 

10. References 

NAPPO PVYN Testing Protocols 

Superficial Necrosis, caused by Virus (PTNRD), UN/ECE paper, 

TRADE/WP.7GE.6/2004/12, 

Appendices 

 - Scoping Survey for PVY Complex 
12

Appendix 1

Scoping Survey for PVY Complex 

1. Purpose: To conduct a scoping survey to assess the presence of different strains of 

PVY and their incidence in seed potatoes in Canada and the United States. The 

specific objectives of the survey are: 

a. to estimate the relative incidence of each strain or novel isolate of PVY (PVYO, 

PVYN, PVYN:O, PVYEU-NTN, PVYNA-NTN, and others), 

b. to assess the correlation between strain type and symptom expression in potato 

2. Principles: To ensure uniformity and comparability of survey results, the survey will 

be conducted in both Canada and the United States to conform to the following 

principles: 

a. every seed producing state/province will be sampled, 

b. the survey will include as many commercial potato cultivars as possible, 

c. every seed farm in all seed producing states/provinces will be sampled, 

d. older field generations of seed potatoes on each farm will be sampled, 

e. the sampling rate in each state/province will be between 100 to 400 tubers per lot., 

f. the number of samples taken in Canada and the US will be proportional to the size 

of their respective seed potato industries, estimated to require about 80,000 tubers 

for Canada and 100,000 tubers for the US. 

g. the survey will utilize an ELISA test (see below) for initial detection of PVY in 

tuber sprouts, 

h. samples will be preserved to allow subsequent strain characterization, 

i. testing will be done on samples representing the 2004 crop and subsequent crops, 

j. samples will be collected randomly within the seed potato lots selected for testing, 

k. results of the survey will be reviewed by September 1, 2005 and subsequent 

years, 

l. confidentiality of individual grower results will be maintained. 

3. Procedure: The survey will be conducted in three stages of testing. 

a. PVY-positive tubers or plants will be selected on the basis of an initial ELISA test 

using monoclonal 4C3. every seed producing state/province will be sampled, 

b. All 4C3-positive tubers/plants will be retested by ELISA using monoclonal 1F5 to 

determine whether the serotype is PVYO or PVYN,

c. The P1 gene of PVY will be amplified by RT-PCR from all 4C3-positive 

tubers/plants and sequenced to determine subtype. Selected PVY isolates 

representing each of the recombinant and strain types will be observed or assayed 

for symptomology on potato foliage and tubers. The following criteria for the 

testing procedures have been adopted to ensure uniformity and comparability of 

results. 

 

4. Sample preparation (although the survey can be conducted using either tuber 
13

sprouts or leaves of grow-out plants, testing of tuber sprouts appears to be most 

feasible and economical). 

a. any method (natural or chemically induced) of breaking tuber dormancy is 

acceptable, 

b. sprouts must be taken from the bud end of the tuber, 

c. one to three sprouts will be tested from each tuber for each test, 

d. sprouts must be at least 0.5 cm but not more than 6.0 cm long, 

e. sprouts from up to three tubers may be combined into a composite sample for the 

initial ELISA test, 

f. a fresh sprout extract will be used for the second ELISA test, 

g. either a third sprout or sap from the second sprout will be used for RT-PCR 

amplification of the PVY P1 gene, 

h. sprout sap to be used for RT-PCR amplification must be kept on ice and used 

within 24 hr. 

5. ELISA. 

a. the initial ELISA test to select PVY infected tubers will utilize monoclonal 

antibody 4C3, 

b. the second ELISA test to determine PVY serotype will utilize monoclonal 

antibody 1F5, 

c. the ELISA tests are to be a triple antibody sandwich (TAS) format, 

d. coating antibody for both ELISA tests will be a polyclonal antibody that reacts 

with known PVY strains, 

e. duplication of test wells is NOT required, 

f. each ELISA plate requires a minimum of one control well containing a PVYO

isolate, one control well containing a PVYN isolate, and four negative control 

wells containing sap from PVY-free sprouts, 

g. all negative control wells must have absorbance values of <0.100 for the results of 

the ELISA plate to be considered valid (the ELISA plate should be blanked on a 

well or wells containing buffer only), 

h. the positive/negative threshold will be 0.100 unless the mean of the negative 

controls is >0.033 in which case the threshold will be 3X the mean of the negative 

controls, 

6. RT-PCR amplification and sequencing 

a. sprout sap will be combined with buffer and spotted in quadruplicate on 

nitrocellulose membranes as specified in the dot blot procedure, 

b. RNA will be extracted from dot blots and cDNA generated by reverse 

transcription using Primer A (Nie and Singh, 2002), 

c. cDNA will be amplified by PCR using Primers S1 and A (Nie and Singh 2002) 

for 30-35 cycles, 

d. sequencing of amplicons will be contracted to a sequencing facility to obtain 

uniform and consistent results, 
14

e. P1 gene sequences will be aligned and analyzed using standard bioinformatics 

protocols will be determined. 

Reference: Nie, X. and Singh, R.P. 2002. A new approach for the simultaneous 

differentiation of biological and geographical strains of potato virus Y by uniplex and 

multiplex RT-PCR. J. Virol. Methods 104:41-54.