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Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease

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Abstract

A virus identified as “apple green crinkle associated virus” (AGCaV) was isolated from Aurora Golden Gala apple showing severe symptoms of green crinkle disease. Evidence was obtained of a potential causal relationship to the disease. The viral genome consists of 9266 nucleotides, excluding the poly(A) tail at the 3’-terminus. It has a genome organization similar to that of members of the species Apple stem pitting virus (ASPV), the type species of the genus Foveavirus, family Betaflexiviridae. ORF1 of AGCaV encodes a replicase-complex polyprotein with a molecular mass of 247 kDa; the proteins of ORFs 2, 3, and 4 (TGB proteins) are estimated to be 25.1 kDa, 12.8 kDa, and 7.4 kDa, respectively; and ORF5 encodes the CP, with an estimated molecular mass of 43.3 kDa. Interestingly, AGCaV utilizes different stop codons for ORF1, ORF3, and ORF5 compared to the ASPV type isolate PA66, and between the two viruses, six distinct indel events were observed within ORF5. AGCaV has four non-coding regions (NCRs), including a 5’-NCR (60 nt), a 3’-NCR (134 nt), and two intergenic (IG) NCRs: IG-NCR1 (69 nt) and IG-NCR2 (91 nt). A conserved stable hairpin structure was identified in the variable 5’-NCR of members of the genus Foveavirus. AGCaV may be a variant or strain of ASPV with unique biological properties, but there is evidence that it may be a distinct putative foveavirus.

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Acknowledgments

We are grateful to the staff of the Diagnostic Section, Sidney Laboratory, Canadian Food Inspection Agency, for generously providing the sample material from the Sidney Virus Repository and information on the disease status and comprehensive results of bioassays and molecular tests conducted over several years.

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Authors and Affiliations

  1. Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, Sidney, BC, V8L 1H3, Canada

    D. James & A. Varga

  2. Ministry of Agriculture, Province of British Columbia, 1690 Powick Road, Kelowna, BC, V1X 7G5, Canada

    G. D. Jesperson

  3. Faculty of Science, Palacký University, 11 Šlechtitelů, 78371, Olomouc, Czech Republic

    M. Navratil & D. Safarova

  4. Department of Primary Industries-Knoxfield, Private Bag 15, Ferntree Gully Delivery Centre, Victoria, 3156, Australia

    F. Constable

  5. New Zealand Institute for Plant and Food Research, Private Bag 1401, 4157, Havelock North, Hawkes Bay, New Zealand

    M. Horner

  6. Washington State University, Prosser, 24106 N. Bunn Road, Prosser, Washington, 99350-8694, USA

    K. Eastwell

  7. Julius Kühn Institut, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, 69221, Dossenheim, Germany

    W. Jelkmann

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  1. D. James
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  2. A. Varga
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  7. M. Horner
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  8. K. Eastwell
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  9. W. Jelkmann
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Correspondence to D. James.

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James, D., Varga, A., Jesperson, G.D. et al. Identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease. Arch Virol 158, 1877–1887 (2013). https://doi.org/10.1007/s00705-013-1678-7

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  • DOI: https://doi.org/10.1007/s00705-013-1678-7

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