Partial nucleotide sequence variability and molecular detection of an isolate of sugarcane mosaic virus in Egypt

摘要

An isolate of sugarcane mosaic virus (ScMV) was obtained from naturally infected sugarcane (Saccharum officinarum L.) plants showing mosaic symptoms collected from different locations in upper Egypt. The reverse-transcription polymerase chain reaction (RT-PCR), immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR), cloning and sequencing were used to detect and molecular characterized the present isolate of ScMV. Approximately 2.0 kb of the 3' terminal region of the ScMV genomewas amplified from the tRNA extracted from sugarcane plant with GeneReleaserTM and the immunocaptured virus using the primers designed by (Yang & Mirkov, 1997). The IC-RT-PCR was found to be more suitable and sensitive detecting ScMV from sugarcane plants. Nucleotide sequence comparative analysis of the partial part from this 2.0 kb of the 3' terminal region of the Egyptian isolate of ScMV genome with other ScMV strains exhibited a homology ranging from 81 to 99% for the 3' terminal region of the ScMV genome in GenBank. The highest nucleotide identity was 99% with the ScMV strain D from Texas, USA. This is the first molecular assay for detecting ScMV strain D in Egypt.