Genetic variability in coat protein gene of sugarcane mosaic virus in Pakistan and its relationship to other strains

Sugarcane mosaic virus (SCMV) is one of the three causative viruses of mosaic in sugarcane, a sugar crop widely grown under tropical and subtropical conditions worldwide. Although molecular characterization of SCMV strains was reported from many countries, strain occurring in Pakistan, a major sugarcane producer has not been reported so far. One hundred and two (102) sugarcane samples from foremost sugarcane growing districts in Pakistan were transcribed by reverse-transcription polymerase chain reaction (RT-PCR) by means of a pair of primers. All of them were found infected with SCMV. The sequences of SCMV coat protein gene amplified in this study varied between 406 and 457 nt. The sequence assessment of 12 Pakistani SCMV isolates revealed extensive range of sequence resemblances, 82-100% nucleotide (nt) and 5.0-95% amino acid (aa) respectively. A deletion of aa residues was observed in the amplified segments of the Pakistani amplicons. 50 SCMV CP sequences (12 from Pakistan and 38 from other sugarcane growing countries) were subjected to phylogenetic and in-silico restriction analyses grouped the isolates mostly in order of their geographical origin. The 12 Pakistani SCMV isolates were included in one group. Nearly 97.0% of isolates from Pakistan have no signs for close association with earlier categorized sugarcane mosaic virus strains SCMV-A, SCMV-B, SCMV-D, SCMV-E, and SCMV-SC described from various countries. Our studies discovered that the sugarcane mosaic in Pakistan is instigated by a new group/strain SCMV-PAK. It is the first representation on the diversity and existence of novel SCMV population in Pakistan.