Genome segment RNA-1 of a flat apple isolate of Cherry rasp leaf virus: nucleotide sequence analysis and RT-PCR detection.
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 identified 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.
James
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Centre for Plant Health, Canadian Food Inspection Agency, Sidney, Canada. jamesd@inspectiongc.ca
Upton
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C
D000595:Amino Acid Sequence; D001483:Base Sequence; D005638:Fruit / Q000821:virology*; D016679:Genome, Viral; D027845:Malus / Q000821:virology; D008969:Molecular Sequence Data; D010942:Plant Viruses / Q000235:genetics*; D027861:Prunus / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction