Analysis of the diversity of African streak mastreviruses using PCR-generated RFLPs and partial sequence data

Maize streak virus (MSV) is the most economically significant member of a d iverse group of African grass-infecting Mastrevirus species in the family G eminiviridae. We designed a single set of degenerate primers which enables the PCR amplification of an approximately 1300 bp DNA fragment spanning bot h conserved (the RepA gene) and variable (the long intergenic region and MP gene) portions of these viruses' genomes. Using restriction fragment lengt h polymorphism (RFLP) analysis of PCR products obtained from 39 MSV, one SS V, and two PanSV isolates, it was possible to both identify the different v irus species, which differ in nucleotide sequence by up to 40%, and to diff erentiate between MSV isolates sharing up to 99% sequence identity. The rel iability of the RFLP data for typing the MSV isolates was verified by the p hylogenetic analysis of the partial genomic nucleotide sequences of a repre sentative subset of the MSV isolates. Based on both the RFLP and sequence d ata, the MSV isolates could be clearly differentiated into the four groups: these were a group of predominantly maize-infecting isolates, and three gr oups containing grass/wheat-infecting isolates. RFLP analysis also revealed a number of mixed virus infections in which, in certain instances, it was possible to identify individual population members. (C) 2001 Elsevier Scien ce B.V. All rights reserved.