Incidence and genetic diversity of apple chlorotic leaf spot virus in Iran

  • Faezehossadat Abtahi
  • Masoud Shams-BakhshEmail author
  • Naser Safaie
  • Abdolbaset Azizi
  • Concepcion Rubies Autonell
  • Claudio Ratti
Original Article


Apple chlorotic leaf spot virus (ACLSV) is one of the most common viruses infecting apple and pear trees, and Iran is among the top ten apple-producing countries in the world. In the present study, incidence and genetic diversity of ACLSV were investigated in the main apple-growing regions of Iran. To achieve this purpose, a total of 1053 leaf samples were collected from orchards located in nine Iranian provinces. ACLSV infection was detected by DAS-ELISA in 48 samples (4.55%) from seven provinces and was confirmed by RT-PCR. Based on the geographical origin, 19 representative isolates were selected for phylogenetic analysis. Nineteen amplicons, with a size of 677 base pairs (bp), containing the 3′ end of the movement protein (MP), the coat protein (CP) gene, and 3′-UTR sequence, were sequenced. Sequence analysis, using data of 45 isolates from 12 different countries, including the 19 Iranian isolates, showed that CP gene among the Iranian isolates were 80–99% identical at both nucleotide and amino acid levels, and these isolates were placed in the B6 (AB326224) and P-205 (D14996) ACLSV groups. This is the first genetic analysis of ACLSV in Iran.


ACLSV Apple Trichovirus DAS-ELISA RT-PCR 



We would like to thank the Iranian Ministry of Science, Research and Technology, for supporting F. Abtahi’s internship in Italy.

Supplementary material

42161_2018_224_MOESM1_ESM.docx (38 kb)
ESM 1 (DOCX 38 kb)


  1. Adams MJ, Antoniw JF, Bar-Joseph M, Brunt AA, Candresse T, Foster GD, Martelli GP, Milne RG, Zavriev SK, Fauquet CM (2004) The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149:1045–1060Google Scholar
  2. Al Rwahnih M, Turturo C, Minafra A, Saldarelli P, Myrta A, Pallas V, Savino V (2004) Molecular variability of Apple chlorotic leaf spot virus in different hosts and geographical regions. J Plant Pathol 86:117–122Google Scholar
  3. Bao Y, Chetvernin V, Tatusova T (2012) Pairwise sequence comparison (PASC) and its application in the classification of filoviruses. Viruses 4:1318–1327CrossRefGoogle Scholar
  4. Chang S, Puryear J, Cairney J (1993) A simple and efficient method for isolating RNA from pine trees. Plant Mol Biol Report 11:113–116CrossRefGoogle Scholar
  5. Chen S, Zhou Y, Ye T, Hao L, Guo L, Fan Z, Li S, Zhou T (2014) Genetic variation analysis of Apple chlorotic leaf spot virus coat protein reveals a new phylogenetic type and two recombinants in China. Arch Virol 159:1431–1438CrossRefGoogle Scholar
  6. Desvignes J, Boyé R (1989) Different diseases caused by the chlorotic leaf spot virus on the fruit trees. Acta Hortic 235:31–38CrossRefGoogle Scholar
  7. Desvignes JC, Boyé R, Cornaggia D, Grasseau N, Hurtt S, Waterworth H (1999) Virus diseases of fruit trees. Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL), Paris, pp 239–252Google Scholar
  8. German S, Candresse T, Lanneau M, Huet J, Pernollet J, Dunez J (1990) Nucleotide sequence and genomic organization of Apple chlorotic leaf spot closterovirus. Virology 179:104–112CrossRefGoogle Scholar
  9. German S, Delbos RP, Candresse T, Lannean L, Dunez J (1997) Complete nucleotide sequence of the genome of a severe cherry isolate of Apple chlorotic leaf spot trichovirus (ACLSV). Arch Virol 142:833–841CrossRefGoogle Scholar
  10. Guo W, Zheng W, Wang M, Xiaohong L, Ma Y, Dai H (2016) Genome sequences of three Apple chlorotic leaf spot virus isolates from Hawthorns in China. PLoS One 11:e0161099. CrossRefGoogle Scholar
  11. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Oxford Journals 41:95–98Google Scholar
  12. Jelkmann W, Kunze L (1995) Plum pseudopox in German plum after infection with an isolate of Apple chlorotic leaf spot virus causing plum line pattern. Acta Hortic 386:122–125CrossRefGoogle Scholar
  13. Keshavarz T, Shams-Bakhsh M (2014) Incidence and distribution of Apple chlorotic leaf spot virus in the main fruit growing areas of Iran. Arch Phytopathol Plant Protect 48:306–312CrossRefGoogle Scholar
  14. Keshavarz T, Shams-Bakhsh M, Norinejad SH (2009) First report of Apple chlorotic leaf spot virus infection of apple trees in Iran. J Plant Pathol 91:233Google Scholar
  15. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
  16. Liu P, Li Z, Song S, Wu Y (2014) Molecular variability of Apple chlorotic leaf spot virus in Shaanxi, China. Phytoparasitica 42:445–454CrossRefGoogle Scholar
  17. Mahfoudhi N, Elair M, Moujahed R, Salleh W, Djelouah K (2013) Occurrence and distribution of pome fruit viruses in Tunisia. Phytopathol Mediterr 52:136–140Google Scholar
  18. Marini D, Gibson P, Scott S (2008) The complete nucleotide sequence of an isolate of Apple chlorotic leaf spot virus from peach (Prunus persica (L.) Batch). Arch Virol 153:1003–1005CrossRefGoogle Scholar
  19. Mathioudakis MM, Maliogka VI, Katsiani AT, Katis NI (2010) Incidence and molecular variability of apple stem pitting and apple chlorotic leaf spot viruses in apple and pear orchards in Greece. J Plant Pathol 92:139–147Google Scholar
  20. Menzel W, Jelkmann W, Maiss E (2002) Detection of four apple viruses by multiplex RT-PCR assays with co-amplification of plant mRNA as internal control. J Virol Methods 99:81–92CrossRefGoogle Scholar
  21. Németh M (1986) Virus, mycoplasma and rickettsia diseases of fruit trees. Akademiai Kiado, BudapestGoogle Scholar
  22. Niu F, Pan S, Wu Z, Jiang D, Li S (2012) Complete nucleotide sequences of the genomes of two isolates of Apple chlorotic leaf spot virus from peach (Prunus persica) in China. Arch Virol 157:783–786CrossRefGoogle Scholar
  23. Paduch-Cichal E, Szyndel MS, Tomala K (2005) Preliminary results of the study on viruses occurring in ‘Mutsu’ apple cultivar trees. Phytopathol Pol 37:87–90Google Scholar
  24. Rana T, Chandel V, Kumar Y, Ram R, Hallan V, Zaidi AA (2010) Molecular variability analyses of Apple chlorotic leaf spot virus capsid protein. J Biosci 35:605–615CrossRefGoogle Scholar
  25. Salem N, Mansour A, Al-Musa A (2005) Viruses of pome fruit trees in Jordan. J Plant Pathol 87:123–126Google Scholar
  26. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Laboratory Press, New YorkGoogle Scholar
  27. Sato K, Yoshikawa N, Takahashi T (1993) Complete nucleotide sequence of the genome of an apple isolate of Apple chlorotic leaf spot virus. J Gen Virol 74:1927–1931CrossRefGoogle Scholar
  28. Song YS, Hong N, Wang LP, Xu WX, Hu HJ, Tian R, Wang GP (2011) Molecular and serological diversity in Apple chlorotic leaf spot virus from sand pear (Pyrus pyrilofia) in China. Eur J Plant Pathol 130:183–196CrossRefGoogle Scholar
  29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  30. Yaegashi H, Isogai M, Tajima H, Sano T, Yoshikawa N (2007) Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of Apple chlorotic leaf spot virus are crucial for infectivity. J Gen Virol 88:2611–2618CrossRefGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Faezehossadat Abtahi
    • 1
  • Masoud Shams-Bakhsh
    • 1
    Email author
  • Naser Safaie
    • 1
  • Abdolbaset Azizi
    • 1
  • Concepcion Rubies Autonell
    • 2
  • Claudio Ratti
    • 2
  1. 1.Plant Pathology Department, Faculty of AgricultureTarbiat Modares UniversityTehranIran
  2. 2.Department of Agricultural Sciences, Plant Pathology and Plant Protection SectionUniversity of BolognaBolognaItaly

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