, Volume 26, Issue 1–2, pp 33–41 | Cite as

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

  • Inas Farouk Fahmy
  • Omnia Taha
  • Abdel Nasser El-Ashry
Original Article


This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.


Rolling circle amplification (RCA) CpCDV Masterviruses Recombination analysis 



This work has been done by the full funding of the Agricultural Genetic Engineering Research Institute. A partial funding from the Science and Development Fund, STDF during a collection mission funded by Project #892 for whitefly and virus collection has contributed in enhancing our virus collection. The thanks also are extended to Eng. Nasser El-Torky, PICO Company Lab Executive Manager for his help in virus collection in Mansoria and El-Behira region.

Supplementary material

13337_2014_246_MOESM1_ESM.docx (14 kb)
(TIF 13.9 kb)
13337_2014_246_MOESM2_ESM.docx (17 kb)
(TIF 16.9 kb)


  1. 1.
    Akhtar S, Khan AJ, Briddon RW. A distinct strain of Chickpea chlorotic dwarf virus infecting pepper in Oman. Plant Dis. 2014;98(2):286–286.CrossRefGoogle Scholar
  2. 2.
    Boulton MI. Functions and interactions of mastrevirus gene products. Physiol Mol Plant Pathol. 2002;60:243–55.CrossRefGoogle Scholar
  3. 3.
    Brown JK, Idris AM, Torres-Jerez I, Banks GK, Wyatt SD. The core region of the coat protein gene is highly useful for establishing the provisional identification of begomoviruses. Arch Virol. 2001;146:1581–98.PubMedCrossRefGoogle Scholar
  4. 4.
    Brunt AA, Crabtree K, Dallwitz MJ, Gibbs AJ, Watson L, Zurcher EJ, editors. Plant viruses online: descriptions and lists from the VIDE database. Version: 20th August 1996. 1996 onwards.
  5. 5.
    Chang CP, et al. A single sequence context cannot satisfy all non-AUG initiator codons in yeast. BMC Microbiol. 2010;10:188.PubMedCentralPubMedCrossRefGoogle Scholar
  6. 6.
    Dry IB, Rigden JE, Krake LR, Mullineaux PM, Rezaian MA. Nucleotide sequence and genome organization of tomato leaf curl geminivirus. J Gen Virol. 1993;74:147–51.PubMedCrossRefGoogle Scholar
  7. 7.
    Elena SF, Agudelo-Romero P, Lalic J. The evolution of viruses in multi-host fitness landscapes. Open Virol J. 2009;3:1–6.PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Erdmann JB, Shepherd DN, Martin DP, Varsani A, Rybicki EP, Jeske H. Replicative intermediates of maize streak virus found during leaf development. J Gen Virol. 2010;91:1077–81.PubMedCrossRefGoogle Scholar
  9. 9.
    Fahmy IF. Molecular characterization of Squash Leaf Curl Virus Egyptian isolate and generation of infectious clone via rolling circle amplification. Egypt J Virol. 2012;19:131–51.Google Scholar
  10. 10.
    Fahmy IF, Taha O, Eldogdog K. Generation of infectious clone of Tomato Yellow leaf Curl Virus Egyptian isolate using the Ф29 DNA polymerase. Egypt J Virol. 2011;18:325–44.Google Scholar
  11. 11.
    Farzadfar Sh, Pourrahim R, Golnaraghi AR, Ahoonmanesh A. PCR detection and partial molecular characterization of Chickpea Chlorotic Dwarf Virus in naturally infected sugar beet plants in Iran. J Plant Pathol. 2008;90(2):247–51.Google Scholar
  12. 12.
    Gibbs MJ, Armstrong JS, Gibbs AJ. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics. 2000;16:573–82.PubMedCrossRefGoogle Scholar
  13. 13.
    Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A. Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res. 2012;166:13–22.PubMedCrossRefGoogle Scholar
  14. 14.
    Hamed AA, Makkouk KM. Occurrence and management of Chickpea chlorotic dwarf virus in chickpea fields in northern Sudan. Phytopathol Mediterr. 2002;41:193–8.Google Scholar
  15. 15.
    Hefferon KL, Moon Y-S, Fan Y. Multi-tasking of nonstructural gene products is required for bean yellow dwarf geminivirus transcriptional regulation. FEBS J. 2006;273:4482–94.PubMedCrossRefGoogle Scholar
  16. 16.
    Hofer JMI, Dekker EL, Reynolds HV, Woolston CJ, Cox BS, Mullineaux PM. Coordinate regulation of replication and virion sense gene expression in wheat dwarf virus. Plant Cell. 1992;4:213–23.PubMedCentralPubMedCrossRefGoogle Scholar
  17. 17.
    Horn NM, Reddy SV, Roberts IM, Reddy DVR. ICTV virus description. Ann Appl Biol. 1993;122:467–79.CrossRefGoogle Scholar
  18. 18.
    Ishibashi K, Meshi T, Ishikawa M. Gaining replicability in a non-host compromises the silencing suppression activity of Tobacco mild green mosaic virus in a host. J Virol. 2011;85(4):1893–5.PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Katoh K, Standley DM. Multiple alignment of DNA sequences with MAFFT. Mol Biol Evol. 2013;30(4):772–80.PubMedCentralPubMedCrossRefGoogle Scholar
  20. 20.
    Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics (Oxf, Engl). 2010;26(15):1899–900.CrossRefGoogle Scholar
  21. 21.
    Katoh K, Asimenos G, Toh H. Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol (Clifton, NJ). 2009;537:39–64.CrossRefGoogle Scholar
  22. 22.
    Kheyr-Pour A, Bendahmane M, Matzeit V, Accotto GP, Crespi S, Navot N, Pichersky E, Zeidan M, Zamir D, Czosneck H. Tomato yellow leaf curl virus: a whitefly transmitted geminivirus with a single genomic component. Virology. 1991;185:151–61.CrossRefGoogle Scholar
  23. 23.
    Kraberger S, Harkins GW, Kumari SG, Thomas JE, Schwinghamer MW, Sharman M, Collings DA, Briddon RW, Martin DP, Varsani A. Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East. Virology. 2013;444:282–91.PubMedCrossRefGoogle Scholar
  24. 24.
    Kraberger S, Mumtaz H, Claverie S, Martin DP, Briddon RW, Varsani A. Identification of an Australian-like dicot-infecting mastrevirus in Pakistan. Arch Virol. 2014. doi: 10.1007/s00705-014-2299-5. .
  25. 25.
    Lazarowitz SG, Pinder AJ, Damsteegt VD, Rogers SG. Maize streak virus genes essential for systemic spread and symptom development. EMBO J. 1989;8:1023–32.PubMedCentralPubMedGoogle Scholar
  26. 26.
    Makkouk KM, Rizkallah L, Kumari SG, Zakiand M, Abul Enein R. First record of Chickpea chlorotic dwarf virus (CpCDV)affecting faba bean (Vicia faba) crops in Egypt New Disease Report. Plant Pathol. 2003;52:413.CrossRefGoogle Scholar
  27. 27.
    Martin DP, Rybicki E. RDP: detection of recombination amongst aligned sequences. Bioinformatics. 2000;16:562–3.PubMedCrossRefGoogle Scholar
  28. 28.
    Martin DP, Willment JA, Billharz R, Velders R, Odhiambo B, Njuguna J, James D, Rybicki EP. Sequence diversity and virulence in Zea mays of maize streak virus isolates. Virology. 2001;288:247–55.PubMedCrossRefGoogle Scholar
  29. 29.
    Martin DP, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics. 2005;21:260–2.PubMedCrossRefGoogle Scholar
  30. 30.
    Martin DP, Briddon RW, Varsani A. Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses. Arch Virol. 2011;156:1463–9.PubMedCrossRefGoogle Scholar
  31. 31.
    Maynard Smith J. Analyzing the mosaic structure of genes. J Mol Evol. 1992;4:126–9.Google Scholar
  32. 32.
    Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol. 2012;1601–7.Google Scholar
  33. 33.
    Mumtaz H, Kumari SG, Mansoor S, Martin DP, Briddon RW. Analysis of the sequence of a dicot-infecting mastrevirus (family Geminiviridae) originating from Syria. Virus Genes. 2011;42(3):422–8.PubMedCrossRefGoogle Scholar
  34. 34.
    Nahid N, Amin I, Mansoor S, Rybicki EP, van der Walt E, Briddon RW. Two dicot-infecting mastreviruses (family Geminiviridae) occur in Pakistan. Arch Virol. 2008;153:1441–51.PubMedCrossRefGoogle Scholar
  35. 35.
    Padidam M, Sawyer S, Fauquet CM. Possible emergence of new geminiviruses by frequent recombination. Virology. 1999;265:218–25.PubMedCrossRefGoogle Scholar
  36. 36.
    Palmer KE, Rybicki EP. The molecular biology of mastreviruses. In: Maramorosch K, Murphy FA, Shatkin AJ, editors. Advances in virus research, vol. 50. San Diego: Academic Press; 1997.Google Scholar
  37. 37.
    Perelygina L, Zhu L, Zurkuhlen H, Mills R, Borodovsky M, Hilliard JK. Complete sequence and comparative analysis of the genome of herpes B virus (Cercopithecine Herpesvirus 1) from a rhesus monkey. J Virol. 2003;77(11):6167–77.PubMedCentralPubMedCrossRefGoogle Scholar
  38. 38.
    Posada D, Crandall KA. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA. 2001;98:13757–62.PubMedCentralPubMedCrossRefGoogle Scholar
  39. 39.
    Ramsell JNE, Boulton MI, Martin DP, Valkonen JPT, Kvarnheden A. Studies on the host range of the barley strain of Wheat dwarf virus using an agroinfectious viral clone. Plant Pathol. 2009;58:1161–9.CrossRefGoogle Scholar
  40. 40.
    Salminen MO, Carr JK, Burke DS, McCutchan FE. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by BOOTSCANning. AIDS Res Hum Retrovir. 1995;11:1423–5.PubMedCrossRefGoogle Scholar
  41. 41.
    Thomas J, Parry J, Schwinghamer M, Dann E. Two novel mastreviruses from chickpea (Cicer arietinum) in Australia. Arch Virol. 2010;155:1777–88.PubMedCrossRefGoogle Scholar
  42. 42.
    Varsani A, Shepherd DN, Monjane AL, Owor BE, Erdmann JB, Rybicki EP, Peterschmitt M, Briddon RW, Markham PG, Oluwafemi S, Windram OP, Lefeuvre P, Lett JM, Martin DP. Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol. 2008;89:2063–74.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Indian Virological Society 2015

Authors and Affiliations

  • Inas Farouk Fahmy
    • 1
  • Omnia Taha
    • 1
  • Abdel Nasser El-Ashry
    • 2
  1. 1.Phytopathogen Vector Interaction Lab, Department of Microbiology, Agricultural Research Center (ARC)Agricultural Genetic Engineering Research InstituteGizaEgypt
  2. 2.Department of Plant Pathology, Faculty of Agriculture, Institute fuer Nutzpflanzenwissenschaften und Ressourcen SchutzUniversity of BonnBonnGermany

Personalised recommendations