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Nucleotide sequence of the carlavirus associated with blueberry scorch and similar diseases

Timothy D. Cavileer^1,

Edward V. Podleckis

¹ Department of Plant Pathology, Rutgers University, New Brunswick, New Jersey 08903, U.S.A.
and² Agriculture Canada, 6660 NW Marine Drive, Vancouver, Canada V6T 1X2

We have synthesized and mapped a library of cDNA clones representing the RNA genome of a strain of blueberry scorch carlavirus (BBScV) associated with a disease known locally, in New Jersey, U.S.A., as Sheep Pen Hill disease. The nucleotide sequence of that strain was determined to be 8514 residues, excluding the poly(A) tail. In addition, cDNA clones representing the 3' terminus of another strain of the virus from the same field were synthesized, mapped and sequenced. The overall identity between sequences of these two strains was approximately 90% spanning the 1634 residue overlap, confirming their identity as distinct strains and not simply different isolates of a single strain. Finally, the coat protein gene of a distinct strain of the virus, isolated from plants with blueberry scorch disease in the Puyallup Valley in Washington State, U.S.A., was cloned from total cDNA by PCR. Sequence analysis revealed that the strain from Washington was more divergent from the two New Jersey strains than they were from each other. Comparisons of these sequences with other carlavirus sequences indicated that BBScV is more closely related to lily symptomless virus and potato virus S than to potato virus M, Helenium virus S, carnation latent virus or poplar mosaic virus. BBScV and potato virus M shared approximately 54% nucleotide sequence identity overall.

Present address: Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho 83843, U.S.A.

Present address: USDA ARS, NGRL, Beltsville, Maryland 20705, U.S.A.

Received 4 August 1993; accepted 10 November 1993.

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