Arch Virol (2005) 150: 1469–1476
Genome segment RNA-1 of a ﬂat apple isolate
of Cherry rasp leaf virus:
nucleotide sequence analysis and RT-PCR detection
and C. Upton
Centre for Plant Health, Canadian Food Inspection Agency, Sidney, Canada
Department of Biochemistry and Microbiology, University of Victoria,
Received August 16, 2004; accepted January 18, 2005
Published online March 24, 2005
Summary. The sequence of the RNA-1 of a ﬂat apple isolate of Cherry rasp
leaf virus (CRLV-FA) was determined using overlapping cDNA fragments.
CRLV-FA RNA-1 consists of 6992 nucleotides (nt), excluding a 3
poly (A) tail.
A single open reading frame (ORF) consisting of 6705 nt was identiﬁed. This
ORF encodes a putative polyprotein consisting of 2235 amino acid (aa) residues,
approximately 249.6 kDa. When compared to CRLV-pot (potato isolate) RNA-1
ORF, 2 deletions of 5 aa and 10 aa (total 15 aa) were observed at the variable
N-terminus of the protease cofactor of CRLV-FA. Non-coding regions were iden-
tiﬁed at the 5
-(142 nt) and 3
-end (145 nt). CRLV-FA and CRLV-pot are isolates
of the same virus with identity levels for the RNA-1 associated nt and deduced
aa of 94% and 95%, respectively. RT-PCR targeting CRLV-FA RNA-1 appear to
be of similar sensitivity and just as reliable as RT-PCR targeting RNA-2.
Cherry rasp leaf virus (CRLV) infects pome fruit (apple) and stone fruit (cherry,
peach) causing serious diseases with symptoms such as reduced fruit quality
and tree vigour [7, 21]. Recently, an isolate of CRLV from potato was detected
and characterized . CRLV is transmitted by the nematode Xiphinema
americanum [8, 22], and has been classiﬁed in the past as a tentative [5, 25],
or deﬁnitive species  of the genus Nepovirus. Sequence analysis of the RNA-2
The sequence appears in the GenBank database as accession number AY764390.