Survey of grapevine pathogens in Pakistan

  • Sunniya Rasool
  • Shagufta NazEmail author
  • Adib Rowhani
  • Alfredo Diaz-Lara
  • Deborah A. Golino
  • Kristen D. Farrar
  • Maher Al RwahnihEmail author
Short Communicatiion


Grapevines from 13 vineyards in Pakistan were surveyed for the prevalence of several pathogens. Using RT-qPCR, 257 samples were tested for 19 viruses, phytoplasmas and Xylella fastidiosa. Prevalent viruses were: grapevine virus A (GVA, 47.8%), grapevine leafroll-associated virus 2 (GLRaV-2, 37.3%), grapevine rupestris stem pitting-associated virus (GRSPaV, 36.1%), and grapevine fleck virus (GFkV, 35%). Other viruses detected were: grapevine leafroll-associated virus 1 (GLRaV-1, 2.3%), grapevine leafroll-associated virus 2RG (GLRaV-2RG, 5%), grapevine leafroll-associated virus 3 (GLRaV-3, 7%), grapevine leafroll-associated virus 4 (GLRaV-4) and its strains (5, 6, and Pr, 16.6%), grapevine leafroll-associated virus 7 (GLRaV-7, 4.2%), grapevine fanleaf virus (GFLV, 11.6%), grapevine virus B (GVB, 4.2%), grapevine virus D (GVD, 0.7%), grapevine virus E (GVE, 1.1%), and grapevine Pinot gris virus (GPGV, 1.9%). Mixed infections were detected in 75.9% of samples. Pathogens tested for, but not detected include GLRaV-4 strains 9 and Car, grapevine red blotch virus (GRBV), tomato ringspot virus (ToRSV), tobacco ringspot virus (TRSV), Arabis mosaic virus (ArMV), grapevine virus F (GVF), phytoplasmas and X. fastidiosa. Additionally, 16 samples were analyzed by high-throughput sequencing (HTS) to confirm RT-qPCR results. In this paper we present an extensive survey for grapevine pathogens and thus the first report of GVA, GVB, GVD, GVE, GRSPaV, GFkV, GLRaV-1, GLRaV-2, GLRaV-2RG, GLRaV-3, GLRaV-4, GLRaV-4 strains 5, 6, and Pr, and GLRaV-7 in Pakistan.


Virus detection RT-qPCR HTS Vitis vinifera 



This publication was made possible by support provided by the U.S. Agency for International Development through the Pakistan – U.S. Science & Technology Cooperation Program. The opinions expressed herein are those of the author(s) and do not necessarily reflect the views of the U.S. Agency for International Development. Additional funding was provided by the Higher Education Commission, Pakistan.

Supplementary material

42161_2019_263_MOESM1_ESM.docx (27 kb)
Supplementary Table 1 (DOCX 26 kb)


  1. Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387(2):395–401CrossRefGoogle Scholar
  2. Al Rwahnih M, Alabi OJ, Westrick NM, Golino D, Rowhani A (2016) Description of a novel monopartite geminivirus and its defective subviral genome in grapevine. Phytopathology 107:240–251CrossRefGoogle Scholar
  3. Al-Tamimi N, Digiaro M, Savino V (1998) Viruses of grapevine in Jordan. Phytopathol Mediterr 37:122–126Google Scholar
  4. Aujla K, Shah N, Ishaq M, Fraooq A (2011) Post-harvest losses the marketing of grapes in Pakistan. Sarhad J Agric 27:485–490Google Scholar
  5. Bashir MK, Schilizzi S, Pandit R (2012) The determinants of rural household food security in the Punjab, Pakistan: An econometric analysis. University of Agriculture, FaisalabadGoogle Scholar
  6. Constable FE, Nicholas P, Rodoni BC (2010) Development and validation of diagnostic protocols for the detection of endemic and exotic pathogens of grapevines. Department of Primary Industries, VictoriaGoogle Scholar
  7. FAO 2017 FAOSTAT. Accessed 01 Mar 2017
  8. Fattouh F, Ratti C, El-Ahwany AMD, Aleem EA, Babini AR, Autonell CR (2014) Detection and molecular characterization of Egyptian isolates of grapevine viruses. Acta Virol 58:137CrossRefGoogle Scholar
  9. Fortusini A, Scattini G, Cinquanta S, Prati S (1996) Natural spread of grapevine leafroll virus 1 (GLRV-1), grapevine leafroll virus 3 (GLRV-3) and grapevine fleck virus (GFkV). Inf Fitopatol 46:39–43Google Scholar
  10. Fuller KB, Alston JM, Golino DA (2015) The economic benefits from virus-screening: a case study of grapevine Leafroll in the north coast of California. Am J Enol Vitic 66:112–119CrossRefGoogle Scholar
  11. GoP (2011) Government of Pakistan. Agricultural Statistics of Pakistan. 2010–2011. Pakistan Bureau of statistics. Islamabad, Pakistan.
  12. Hodgetts J, Boonham N, Mumford R, Dickinson M (2009) Panel of 23S rRNA gene-based real-time PCR assays for improved universal and group-specific detection of phytoplasmas. Appl Environ Microbiol 75(9):2945–2950CrossRefGoogle Scholar
  13. Jaskani MJ, Abbas H, Sultana R, Khan MM, Qasim M, Iqrar AK (2008) Effect of growth hormones on micropropagation of Vitis Vinifera L. cv. Perlette. Pak J Bot 40:105–109Google Scholar
  14. Lima M, Alkowni R, Uyemoto JK, Rowhani A (2009) Genomic study and detection of a new variant of grapevine rupestris stem pitting associated virus in declining California pinot noir grapevines. J Plant Pathol 91:155–162Google Scholar
  15. Martelli GP (2014) Directory of virus and virus-like diseases of the grapevine and their agents. J Plant Pathol 96:1–136Google Scholar
  16. Martelli GP (2017) An overview on grapevine viruses, viroids, and the diseases they cause. In: Meng B, Martelli GP, Golino DA, Fuchs M (eds) Grapevine viruses: molecular biology, diagnostics and management. Springer, Cham, pp 31–46CrossRefGoogle Scholar
  17. Martelli GP, Conti M, Minafra A. (2001) Grapevine virus A. Descriptions of plant viruses No 383Google Scholar
  18. Meng B, Gonsalves D (2007) Grapevine rupestris stem pitting-associated virus: a decade of research and future perspectives. Plant Viruses 1:52–62Google Scholar
  19. Osman F, Rowhani A (2006) Application of a spotting sample preparation technique for the detection of pathogens in woody plants by RT-PCR and real-time PCR (TaqMan). J Virol Methods 133:130–136CrossRefGoogle Scholar
  20. Osman F, Rowhani A (2008) Real-time RT-PCR (TaqMan®) assays for the detection of viruses associated with rugose wood complex of grapevine. J Virol Methods 154:69–75CrossRefGoogle Scholar
  21. Osman F, Leutenegger C, Golino D, Rowhani A (2007) Real-time RT-PCR (TaqMan®) assays for the detection of grapevine Leafroll associated viruses 1–5 and 9. J Virol Methods 141:22–29CrossRefGoogle Scholar
  22. Osman F, Olineka T, Hodzic E, Golino D, Rowhani A (2012) Comparative procedures for sample processing and quantitative PCR detection of grapevine viruses. J Virol Methods 179:303–310CrossRefGoogle Scholar
  23. Prabha K, Baranwal VK, Jain RK (2013) Applications of next generation high throughput sequencing technologies in characterization, discovery and molecular interaction of plant viruses. Indian J Virol 24(2):157–165CrossRefGoogle Scholar
  24. Rasool S, Naz S, Rowhani A, Golino DA, Westrick NM, Farrar KD, Al Rwahnih M (2017) First report of grapevine pinot gris virus infecting grapevine in Pakistan. Plant Dis 101:1958CrossRefGoogle Scholar
  25. Reisch BI, Owens CL, Cousins PS (2012) Grape. In: Badenes ML, Byrne DH (eds) Fruit Breeding. Handbook of Plant Breeding, vol 8. Springer, Boston, pp 225–262Google Scholar
  26. Ricketts KD, Gomez MI, Atallah SS, Fuchs MF, Martinson TE, Battany MC, Bettiga LJ, Cooper ML, Verdegaal PS, Smith RJ (2015) Reducing the economic impact of grapevine leafroll disease in California: identifying optimal disease management strategies. Am J Enol Vitic 66:138–147CrossRefGoogle Scholar
  27. Rowhani A, Zhang YP, Chin H, Minafra A, Golino DA, Uyemoto JK (2000) Grapevine rupestris stem pitting associated virus: population diversity, titer in the host and possible transmission vector. Extended abstracts of the 13th meeting of the International Council for the Study of viruses and virus-like diseases of the grapevine (ICVG), march 12–18, 2000, Adelaide, Australia, p 37Google Scholar
  28. Schaad NW, Opgenorth D, Gaush P (2002) Real-time polymerase chain reaction for one-hour on-site diagnosis of Pierce's disease of grape in early season asymptomatic vines. Plant Dis 92:721–728Google Scholar
  29. Sharma AM, Baraff B, Hutchins JT, Wong MK, Blaisdell GK, Cooper ML, Daane KM, Almeida RP (2015) Relative prevalence of grapevine leafroll associated virus species in wine grape-growing regions of California. PLoS One 10:e0142120CrossRefGoogle Scholar
  30. Tatusova TA, Madden TL (1999) BLAST 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174:247–250CrossRefGoogle Scholar
  31. Uddin M, Shah M, Rahman K, Alam R, Rauf MA (2011) Evaluation of local and exotic grapes germplasm at Mingora, Swat. Sarhad J Agric 27:553–556Google Scholar
  32. Vončina D, Al-Rwahnih M, Rowhani A, Gouran M, Almeida RPP (2017) Viral diversity in autochthonous Croatian grapevine cultivars. Plant Dis 101:1230–1235CrossRefGoogle Scholar
  33. Walton VM, Pringle KL (2004) Vine mealybug, Planococcus ficus (Signoret) (Hemiptera: Pseudococcidae), a key pest in South African vineyards. A review. S Afr J Enol Vitic 25:54–62Google Scholar

Copyright information

© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2019
corrected publication 2019

Authors and Affiliations

  • Sunniya Rasool
    • 1
  • Shagufta Naz
    • 1
    Email author
  • Adib Rowhani
    • 2
  • Alfredo Diaz-Lara
    • 2
  • Deborah A. Golino
    • 2
  • Kristen D. Farrar
    • 3
  • Maher Al Rwahnih
    • 2
    Email author
  1. 1.Department of BiotechnologyLahore College for Women UniversityLahorePakistan
  2. 2.Department of Plant PathologyUniversity of California-DavisDavisUSA
  3. 3.Foundation Plant ServicesDavisUSA

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