Molecular identification and phylogenetic characterization of new A-strain isolates of Maize streak virus from western Ethiopia

Abstract The A-strain of Maize streak virus (MSV) causes maize streak disease (MSD) which is a major biotic threat to maize production in sub-Saharan Africa. Previous studies have described different maize streak virus (MSV) strains of economic importance from southern and eastern African countries, and how eastern African regions are hubs for MSV diversification. Despite these efforts, and lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, field sampling of maize plants and wild grasses with visible MSD symptoms were carried out in western Ethiopian regions of Gambela, Oromia, and Benishangul-Gumuz, during the maize growing season of 2019. The complete genomes of MSV isolates (n = 60) were cloned and Sanger sequenced. We use a model based phylogenetic approach to analyse 792 full MSV genome sequences available in the GenBank together with newly recovered genomes from Ethiopia to determine their subtypes and recombinant lineages. Of the 127 fields accessed, MSD prevalence was highest at 96% in Gambela region, and lowest in Oromia at 66%. Highest mean symptom severity of 4/5, (where 5 is the highest and 1 the lowest) was observed for both Gambela and Benishangul-Gumuz. Our results show that these new MSV isolates belong in the recombinant lineage V of the A 1 subtype with the widest dissemination, and economic significance in the sub-Saharan Africa and the adjacent Indian Ocean islands.