Genome segment RNA-1 of a flat apple isolate of Cherry rasp leaf virus: nucleotide sequence analysis and RT-PCR detection

Abstract

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.

DOI: 10.1007/s00705-005-0503-3

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@article{James2005GenomeSR, title={Genome segment RNA-1 of a flat apple isolate of Cherry rasp leaf virus: nucleotide sequence analysis and RT-PCR detection}, author={Delano James and Carol Upton}, journal={Archives of Virology}, year={2005}, volume={150}, pages={1469-1476} }