Skip to main content


  • Short report
  • Open Access

Differential pathogenicity of two different recombinant PVYNTN isolates in Physalis floridana is likely determined by the coat protein gene

Virology Journal20118:207

  • Received: 22 November 2010
  • Accepted: 7 May 2011
  • Published:


A previous study has identified two types of recombinant variants of Potato virus Y strain NTN (PVYNTN) in China and sequenced the complete genome of the variant PVYNTN-HN2. In this study, the complete genome of isolate PVYNTN-HN1 was fully sequenced and analyzed. The most striking difference between the two variants was the location of recombinant joint three (RJ3). In PVYNTN-HN1, like other typical European-PVYNTN isolates such as PVYNTN-Hun, the RJ3 was located at nucleotide (nt) 9183, namely the 3' proximal end of the CP gene (nt. 8571-9371), thus leading to most (the first 613 nucleotides from the 5' proximal end) of the CP gene (801 bp) with a PVYN origin and PVYN-serotype; whereas in contrast, the RJ3 in PVYNTN-HN2 was located at nt 8572, consequently leading to a CP gene of PVYO origin and PVYO-serotype. The varied genome composition among PVYO, PVYN, PVYN:O, PVYNTN-HN1 and PVYNTN-HN2 made them useful for the investigation of possible roles of gene segment(s) in symptom formation on host plants. When Physalis floridana plants were infected with different PVY isolates, two types of symptoms were induced. PVYN and PVYNTN-HN1 induced mild symptoms (mainly mild mottling) whereas PVYO, PVYN:O and PVYNTN-HN2 induced serve symptoms including leaf and stem necrosis, leaf-drop and stunting. These results, together with a previous study using artificial PVY chimeras, demonstrate that the CP gene, especially the 5' proximal segment (nt 8572-9183), and/or CP likely determine the pathogenicity of PVY in P. floridana.


  • Symptom Formation
  • Veinal Necrosis
  • Stem Necrosis
  • Potato Tuber Necrotic Ringspot Disease
  • Necrosis Strain


Potato virus Y (PVY) is the type species of the Potyvirus genus in the Potyviridae family [1]. It infects a number of plant species in the nightshade family (Solanaceae) and causes a wide range of symptoms from symptomless to mosaic, mottling, lesions, stunting, necrosis and plant death, depending on the plant species, the cultivar, the virus strain and isolate [1]. PVY possesses a single-stranded positive RNA genome comprised of approximately 9700 nucleotides that encode a polyprotein of approximately 3061 amino acids [2]. The polyprotein undergoes proteolysis to form 10 mature proteins with different functions including replication, transportation and spread of the virus [1, 2]. Many strains/substrains of PVY have been recognized according to the primary hosts and host reactions. For the potato-infecting PVY, the ordinary strain (PVYO), the tobacco veinal necrosis strain (PVYN) and the potato stipple streak strain (PVYC) are the first ones to be recognized [1], followed by the potato tuber necrosis strain (PVYNTN) and the recombinant N:O/Wilga group (PVYN:O or PVYN-Wilga) [35]. PVYNTN is characterized by its ability to induce potato tuber necrotic ringspot disease (PTNRD) in sensitive potato cultivars [57], whereas PVYN:O is defined by its reaction to PVYO-specific antibody (i.e., PVYO-serotype) but causing veinal necrosis on tobacco plants (i.e., PVYN pathotype) [5, 8]. Two types of PVYNTN, one recombinant and the other non-recombinant, have been identified [4, 7, 9]. The former is represented by PVYNTN-Hun [10] and has been referred to as European (Eu)-PVYNTN[7, 1113], and the latter is represented by PVYNTN-Tu 660 [7] and has been referred to as North American (NA)-PVYNTN[7, 11, 12, 14]. Both Eu-PVYNTN and NA-PVYNTN react to PVYN-specific antibody [11, 13]. Recently, a new recombinant PVYNTN variant type has been identified in Syria [15, 16] and China [9]. The variant type that includes the isolates PVYNTN-NW[16] and PVYNTN-HN2 [9] reacts to PVYO-antibody and induces veinal necrosis on tobacco and PTNRD on sensitive potato cultivars [9, 16]. Reverse transcription-PCR (RT-PCR) based genotyping has been successfully used to characterize the genome features of the Eu-PVYNTN-like isolate PVYNTN-HN1 and the PVYNTN-NW-like isolate PVYNTN-HN2 in China [9]. Here we report the differential responses of Physalis floridana to PVYNTN-HN1 and PVYNTN-HN2 infections. PVYNTN-HN1 and PVYN induced mottling on P. floridana whereas PVYNTN-HN2, PVYO and PVYN:O induced severe symptoms including leaf and stem necrosis, leaf-drop and stunting. The results, together with the genome make-ups of various PVY isolates, suggest that the CP gene plays a significant role in symptom induction in P. floridana, consistent with the results reported by Bukovinszki et al.[17].

The greenhouse maintained PVY isolates PVYNTN-HN1 (formerly PVY sample 1 [9]), PVYNTN-HN2, PVYN-Jg, PVYO-RB and PVYN:O-Mb58 in 'Russet Burbank' plants/tubers [5, 7, 9, 1113] were used in this study. PVYNTN-HN1 and PVYNTN-HN2 were obtained in China [9], while the rest were from Canada [5, 7, 1113]. All isolates have been characterized molecularly by P1 gene- and recombinant joint (RJ)-based RT-PCR assays [12, 13], pathologically by tobacco- and potato-based bioassays, and serologically by PVYO- and PVYN-antibody-based ELISA assays [5, 7, 9, 1113, 18]. Moreover, except for PVYNTN-HN1, all of the isolates have been sequenced fully (PVYNTN-HN-2, PVYN-Jg, PVYO-RB) or partially (PVYN:O-Mb58) (accession numbers are HM367076, AY166867, GQ200836, AY745493 for PVYO-RB, PVYN-Jg, PVYNTN-HN-2, and PVYN:O-Mb58 respectively). To better understand the isolate PVYNTN-HN1, especially to reveal the exact nucleotide locations of the recombinant joints that had been detected by RT-PCR [9], the complete genome of PVYNTN-HN1 was sequenced. The same nine sets of PCR primers (for primer sequences, see reference [7]) that had been used to clone/sequence various isolates of PVY [5, 7, 9, 18] were used. Each primer pair resulted in a DNA fragment of 1.0 to 1.3 kb, overlapping with adjacent fragments with approximately 100 bp at each end. Each fragment was cloned into a pGM-T cloning vector (TIANGEN Biotech, Beijing, China) according to the manufacturer's instructions; and two clones of each fragment were sequenced from both forward and reverse directions using the universal T7 promoter and SP6-promoter primers at the Sangon Biological Engineering Technology & Services Co. Ltd (Shanghai, China). The complete genome sequence (GenBank accession number HQ631374) was confirmed by re-sequencing overlapping cDNA clones obtained from a separate experiment from RNA isolated from PVYNTN-HN1 infected tobacco leaves. Sequence identities were analyzed using BLAST ( For detection of the recombinant events, complete nucleotide sequences of various PVY isolates were aligned using ClustalW2 ( [19]. The aligned sequences served as inputs for similarity scanning using the program SimPlot [20, generously provided by the author at]. The resulting similarities were plotted along the nucleotide sequences of the virus genome.

As anticipated, PVYNTN-HN1 shared highest sequence identities with PVYNTN-Hun, a representative of typical Eu-PVYNTN, at both complete nucleotide and polyprotein levels at 99.2% and 99.1%, respectively. It was followed by PVYNTN-HN2/PVYNTN-NW, PVYN:O, PVYN and PVYO, represented by isolates PVYNTN-HN2, PVYN:O-Mb112, PVYN-N605 and PVYO-RB, respectively (Table 1). The sequence identities between PVYNTN-HN1 and PVYN-Jg, a NA- PVYN[7, 11], were 90.9% and 95.9% at the complete nucleotide and polyprotein levels, respectively (Table 1). As expected, the sequence identities between PVYNTN-HN1 and PVYN:O-Mb58 (accession number AY745493, partial length) were similar to that between PVYNTN-HN1 and PVYN:O-Mb112 (data not shown). Further comparison of PVYNTN-HN1 with PVYNTN-HN2 at mature protein level revealed that the two shared high sequence identities for all proteins (97.8 - 100%) but the CP (Table 1), which was similar to that exhibited in PVYNTN-Hun vs PVYNTN-HN2 [9]. Sequence screening of PVYNTN-HN1 against PVYO (e.g., PVYO-RB) and PVYN (e.g., PVYN-605 or PVYN-Jg) using SimPlot [20] revealed three recombinant joints at nt 2419, 5844 and 9183 in PVYNTN-HN1 genome (Figure 1D), resulting from the genome recombination between PVYN and PVYO. In contrast, the RJs in PVYNTN-HN2 were located at nt 2521, 5867 and 8572 (Figure 1D) [9]. PVYNTN-HN1 shares identical RJs with PVYNTN-Hun (data not shown). The location of RJ3 in PVYNTN-HN1 and PVYNTN-Hun at nt 9183, namely the 3' proximal end of CP gene (nt 8571-9371), led to most (the first 613 nt from the 5' proximal end) of the 801-bp-long CP gene of a PVYN origin, which eventually resulted in a PVYN-serotype of these isolates [5, 7, 9]. In contrast, the RJ3 in PVYNTN-HN2/PVYNTN-SYR-NB-16N (accession number AB270705) at nt 8572, namely the 5'end of the CP gene, led to the complete CP gene of a PVYO origin, which further resulted in a PVYO-serotype [9, 15]. One RJ, namely RJ1, was present in PVYN:O isolates including PVYN:O-Mb112 and PVYN:O-Mb58 at nt 2397 [5] (Figure 1D), resulting in a recombinant genome in which the segment prior to the RJ was from PVYN and the remainder from PVYO[5].
Table 1

Identities between isolate PVYNTN-HN1 and other isolates of Potato virus Y (PVY) at both nucleic acid and protein levels



Sequence Identity (%) (Nucleic acid, Protein)


Gene nucleotide, size (bp)

Protein size (aa)

PVYO-RB (HM367076)

PVYN-605 (X97895)

PVYN-Jg (AY166867)

PVYNTN-Hun (M95491)

PVYN:O-Mb112 (AY745491)

PVYNTN-HN2 (GQ200836)

5' UTR

1-188, 188


66.0, -

100, -

85.6, -

100, -

100, -

99.5, -


189-1013, 825


73.0, 71.3

99.3, 99.6

92.2, 91.3

98.7, 98.2

99.6, 100

98.9, 100


1014-2408, 1395


82.2, 90.5

98.8, 99.4

92.6, 96.8

99.1, 99.1

98.4, 99.4

98.4, 98.9


2409-3503, 1095


97.3, 98.6

84.7, 92.6

84.6, 92.3

99.4, 99.7

99.1, 99.7

96.3, 97.8


3504-3659, 156


97.4, 100

81.4, 84.6

82.1, 86.5

99.4, 100

100, 100

98.1, 98.1


3660-5561, 1902


97.3, 99.1

84.1, 95.7

84.1, 95.7

99.6, 99.5

99.3, 99.5

98.7, 99.7


5562-5717, 156


95.5, 100

82.1, 90.4

79.5, 90.4

100, 100

100, 100

99.4, 98.1


5718-6281, 564


86.9, 92.0

97.0, 99.5

95.6, 97.3

98.9, 99.5

87.8, 94.7

97.9, 99.5


6282-7013, 732


80.9, 93.6

99.3, 98.2

97.0, 98.8

99.2, 98.8

80.6, 92.2

99.0, 99.2


7014-8570, 1557


83.5, 93.6

98.8, 99.0

97.6, 98.7

98.7, 98.7

84.9, 94.4

98.2, 99.0


8571-9371, 801


90.8, 92.9

97.5, 98.9

96.5, 98.9

99.4, 98.9

91.4, 94.4

91.6, 94.0

3' UTR

9372-9702, 331


98.2, -

84.0, -

85.8, -

99.1, -

98.8, -

99.1, -

Full length

1-9702, 9702


87.9, 92.8

93.2, 97.3

90.9, 95.9

99.2, 99.1

94.1, 97.4

97.7, 98.7

Previous study has revealed the pathotypes of PVYNTN-HN1 and PVYNTN-HN2 on tobacco and potato [9]. To further characterize the biological properties of these isolates, and, moreover, to investigate whether the different RJ3 sites, namely different CP gene types, play a role in symptom induction in different plant species, tobacco (cv. 'Samsun'), potato (cv. 'Yukon Gold') and Physalis floridana plants were mechanically inoculated with PVYNTN-HN1, PVYNTN-HN2, PVYN-Jg, PVYO-RB, and PVYN:O-Mb58 as described previously [9]. Mock (buffer)-inoculated plants were used as a healthy control. As shown in Figure 1A, petiole and stem necrosis occurred on tobacco plants 15 days after inoculation with PVYN-Jg, PVYN:O-Mb58, PVYNTN-HN1 or PVYNTN-HN-2. Veinal necrosis also developed on these plants. On the other hand, the PVYO-infected plants only developed mosaic symptoms on the leaves and were free of veinal, petiole and stem necrosis (Figure 1A). No symptoms were observed on the mock-inoculated plants. Various studies have indicated that HC-Pro plays an important role in necrosis development on tobacco plants [5, 21, 22]. All isolates but PVYO-RB possessed a PVYN-type of HC-Pro gene [5, 7, 9, 18] (Figure 1D), and therefore induced PVYN-like symptoms including veinal/petiole/stem necrosis on tobacco plants. When inoculated to 'Yukon Gold' plantlets (5-leaf-stage), the isolates induced varied foliar symptoms including mild mottling (PVYN-Jg), mosaic (PVYN:O-Mb58) and severe mosaic/stunting/leaf deformation (PVYO-RB, PVYNTN-HN1 and PVYNTN-HN2) (data not shown), consistent with the previous report [9]. No visible symptoms were observed on potato tubers produced from plants infected with PVYN-Jg, PVYO-RB or PVYN:O-Mb58; and in contrast, distinct necrotic ringspots were observed on potato tubers harvested from plants infected with PVYNTN-HN1 or PVYNTN-HN2 (Figure 1B), thus confirming that both types of recombinant PVYNTN isolates are capable of inducing PTNRD in sensitive potato cultivars.
Figure 1
Figure 1

Symptoms induced by different isolates of Potato virus Y (PVY) on tobacco, potato and Phyalis floridana. A. Symptoms on tobacco (Nicotiana tabacum cv. 'Samsun') plants 15 days after inoculation. B. Symptoms on potato (Solanum tuberosum cv. 'Yukon Gold') tubers harvested from plants 90 days after inoculation. C. Symptoms on P. floridana 25 days after inoculation. D. Summary of genome composition, recombinant joint (RJ) locations, CP gene type, HC-Pro gene type and major symptoms of PVY isolates. Isolates used for the experiments are PVYO-RB, PVYN-Jg, PVYN:O-Mb58, PVYNTN-HN1 and PVYNTN-HN2.

It has been known that PVYO induces necrosis in Physalis floridana, whereas PVYN incites mottling in this species [1]. Using N/O hybrids comprised of the chimeric genome of PVYN-N605 [23] and PVYO, the symptom formation on P. floridana due to PVY infection was mapped to the CP gene region [17]. Because of the varied genome compositions among the isolates (Figure 1D), they could be used to investigate the putative role of genome segment(s) of PVY in symptom development on P. floridana, as done on tobacco [5, 24]. Severe symptoms including leaf and stem necrosis, leaf-drop and stunting were observed on P. floridana plants infected with PVYO-RB, PVYN:O-Mb58 and PVYNTN-HN2 three weeks after inoculation (Figure 1C), and as time progressed, the symptoms became more distinct. The isolate PVYN:O-Mb58 led to plant death five weeks after the inoculation. On the other hand, mild symptoms, mainly mottling, were observed on PVYN-Jg and PVYNTN-HN1 infected P. floridana plants (Figure 1C). Taken together, it can be concluded that the CP gene originated from PVYO is likely responsible for the severe symptoms in PVYO-, PVYN:O- or PVYNTN-HN2-infected P. floridana plants. These results, together with the results obtained using artificial PVY chimeras [17], demonstrate that the CP gene, especially the 5' proximal segment (nt 8572-9183) of the gene, plays a critical role in symptom formation in P. floridana upon PVY infection, and determines the pathoginicity of PVY isolates. The 3' proximal segment of NIb gene (nt 8136-8570) does not appear to be involved in the symptom formation in P. floridana as suggested by Bukovinszki et al.[17]. It is also noteworthy that the different symptoms incited by different PVY types/isolates in tobacco, potato and P. floridana can be used to uncover the genome compositions of the virus.



The research was supported by the Ministry of Science and Technology of China under the project # 20073346 to XX and CH and by Agriculture and Agri-Food Canada (AAFC) under the projects #50 and #1389 to XN. XH was a receipt of the Ministry of Education of China-AAFC Ph.D. Student Internship Program (2007-2008); XN is an adjunct professor at Hunan Agricultural University.

Authors’ Affiliations

Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Provincial Engineering Research Center for Potatoes,College of Horticulture and Landscape,Hunan Agricultural University, Changsha, Hunan, 410128, China
Potato Research Centre, Agriculture and Agri-Food Canada, P.O. Box 20280, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada


  1. Shukla DD, Ward CW, Brunt AA: The Potyviridae. Wallingford, Oxon, UK: CAB International; 1994.Google Scholar
  2. Riechmann JL, Laín S, García JA: Highlights and prospects of potyvirus molecular biology. J Gen Virol 1992, 73: 1-16. 10.1099/0022-1317-73-1-1View ArticlePubMedGoogle Scholar
  3. Chrzanowska M: New isolates of the necrotic strain of potato virus Y (PVY N ) found recently in Poland. Potato Res 1991, 34: 178-182.View ArticleGoogle Scholar
  4. Glais L, Tribodet M, Kerlan C: Genomic variability in Potato potyvirus Y (PVY): evidence that PVY N W and PVY NTN variants are single to multiple recombinants between PVY O and PVY N isolates. Arch Virol 2002, 147: 363-378. 10.1007/s705-002-8325-0View ArticlePubMedGoogle Scholar
  5. Nie X, Singh RP, Singh M: Molecular and pathological characterization of N:O isolates of the Potato virus Y from Manitoba, Canada. Can J Plant Pathol 2004, 26: 573-583. 10.1080/07060660409507178View ArticleGoogle Scholar
  6. Le Romancer M, Kerlan C, Nedellec M: Biological characterization of various geographical isolates of potato virus Y inducing superficial necrosis on potato tubers. Plant Pathol 1994, 43: 138-144. 10.1111/j.1365-3059.1994.tb00563.xView ArticleGoogle Scholar
  7. Nie X, Singh RP: Evolution of North American PVY NTN strain Tu 660 from local PVY N by mutation rather than recombination. Virus Genes 2003, 26: 39-47. 10.1023/A:1022326021195View ArticlePubMedGoogle Scholar
  8. Singh RP, McLaren DL, Nie X, Singh M: Possible escape of a recombinant isolate of Potato virus Y by serological indexing and methods of its detection. Plant Dis 2003, 87: 679-685. 10.1094/PDIS.2003.87.6.679View ArticleGoogle Scholar
  9. Hu X, He C, Xiao Y, Xiong X, Nie X: Molecular characterization and detection of recombinant isolates of Potato virus Y from China. Arch Virol 2009, 154: 1303-1312. 10.1007/s00705-009-0448-zView ArticlePubMedGoogle Scholar
  10. Thole V, Dalmay T, Burgyan J, Balazs E: Cloning and sequencing of potato virus Y (Hungarian isolate) genomic RNA. Gene 1993, 123: 149-156. 10.1016/0378-1119(93)90118-MView ArticlePubMedGoogle Scholar
  11. Nie X, Singh RP: Probable geographical grouping of PVY N and PVY NTN based on sequence variation in P1 and 5'-UTR of PVY genome and methods for differentiating North American PVY NTN . J Virol Methods 2002, 103: 145-156. 10.1016/S0166-0934(02)00023-XView ArticlePubMedGoogle Scholar
  12. Nie X, Singh RP: 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 2002, 104: 41-54. 10.1016/S0166-0934(02)00037-XView ArticlePubMedGoogle Scholar
  13. Nie X, Singh RP: Specific differentiation of recombinant PVY N:O and PVY NTN strains by multiplex RT-PCR. J Virol Methods 2003, 113: 69-77. 10.1016/S0166-0934(03)00221-0View ArticlePubMedGoogle Scholar
  14. Piche LM, Singh RP, Nie X, Gudmestad NC: Diversity among Potato virus Y isolates obtained from potatoes grown in the United States. Phytopathology 2004, 94: 1368-1375. 10.1094/PHYTO.2004.94.12.1368View ArticlePubMedGoogle Scholar
  15. Chikh Ali M, Maoka T, Natsuaki KT: The occurrence and characterization of new recombinant isolates of PVY displaying shared properties of PVY NW and PVY NTN . J Phytopath 2007, 155: 409-415. 2007 10.1111/j.1439-0434.2007.01251.xView ArticleGoogle Scholar
  16. Chikh Ali M, Maokac T, Natsuakib T, Natsuaki KT: PVY NTN-NW , a novel recombinant strain of Potato virus Y predominating in potato fields in Syria. Plant Pathol 2010, 59: 31-41. 10.1111/j.1365-3059.2009.02174.xView ArticleGoogle Scholar
  17. Bukovinszki A, Gotz R, Johansen E, Maiss E, Balazs E: The role of the coat protein region in symptom formation on Physalis floridana varies between PVY strains. Virus Res 2007, 127: 122-125. 10.1016/j.virusres.2007.03.023View ArticlePubMedGoogle Scholar
  18. Nie B, Singh M, Sullivan A, Singh RP, Xie C, Nie X: Recognition and molecular discrimination of severe and mild PVY O variants of Potato virus Y in potatoes in New Brunswick, Canada. Plant Dis 2011, 95: 113-119. 10.1094/PDIS-04-10-0257View ArticleGoogle Scholar
  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: ClustalW and ClustalX version 2. Bioinformatics 2007, 23: 2947-2948. 10.1093/bioinformatics/btm404View ArticlePubMedGoogle Scholar
  20. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 1999, 73: 152-160.PubMed CentralPubMedGoogle Scholar
  21. Tribodet M, Glais L, Kerlan C, Jacquot E: Characterization of Potato virus Y (PVY) molecular determinants involved in the vein necrosis symptom induced by PVY N isolates in infected Nicotiana tabacum cv. Xanthi. J Gen Virol 2005, 86: 2101-2105. 10.1099/vir.0.80926-0View ArticlePubMedGoogle Scholar
  22. Hu X, Meacham T, Ewing L, Gray SM, Karasev AV: A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco. Virus Res 2009, 143: 68-76. 10.1016/j.virusres.2009.03.008View ArticlePubMedGoogle Scholar
  23. Jakab G, Droz E, Brigneti G, Baulcombe D, Malnoe P: Infectious in vivo and in vitro transcripts from a full-length cDNA clone of PVY-N605, a Swiss necrotic isolate of potato virus Y. J Gen Virol 1997, 78: 3141-3145.View ArticlePubMedGoogle Scholar
  24. Ramírez-Rodríguez V, Aviña-Padilla K, Frías-Treviño G, Silva-Rosales L, Martínez-Soriano J: Presence of necrotic strains of Potato virus Y in Mexican potatoes. Virology J 2009, 6: 48. 10.1186/1743-422X-6-48View ArticleGoogle Scholar


© Hu et al; licensee BioMed Central Ltd. 2011

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.