Identification of two Sugarcane Mosaic Virus (SCMV) variants from naturally infected sugarcane crop in Pakistan

Leaf samples of sugarcane were collected from symptomatic and non-symptomatic plants. total rna was extracted and purified from sugarcane leaves samples. presence of mosaic virus was confirmed by rt-pcr amplification using primers designed to the conserved regions of the coat protein genes of sugarcane mosaic virus (scmv). an amplification product of expected size (approx. 900 bp) was achieved from symptomatic samples but no amplification was detected from non-symptomatic plant samples. rt-pcr amplified dna fragments were cloned and sequenced in both directions. dna sequence from two virus isolates from sugarcane cultivars cssg676 and cssg668 showed highest level of sequence identity (97% and 96%,respectively) to scmv (bundaberg isolate),indicating that the virus isolates infecting sugarcane varieties are variants of scmv in pakistan.