No abstract

Maize lethal necrosis disease (MLN) is an emerging disease in East Africa caused by the introduction of Maize chlorotic mottle virus (MCMV). Recent activity seeking to limit spread of the disease is reliant on effective diagnostics. Traditional diagnostics applied on samples with typical field symptoms of MLN have often given negative results using ELISA or PCR for MCMV and Sugarcane mosaic virus (SCMV). Samples collected in the field with typical MLN symptoms were examined using next generation sequencing (NGS). SCMV was found to be more prevalent than suggested by targeted diagnostics. Additionally, the panel of samples were found to be infected with a range of other viruses, seven of which are described here for the first time. Although not previously identified in the region, Maize yellow mosaic virus (MYMV) was the most prevalent virus after MCMV. The development of targeted diagnostics for emerging viruses is complicated when the extent of field variation is unknown, something that can be negated by using NGS methods. As a result we explored MinION technology which may be more readily deployable in resource poor settings. The results show that this sequencer can diagnose known viruses and future iterations have the potential to identify novel viruses.

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 MSV strains of economic importance from southern and eastern African countries, and how eastern African regions are hubs for MSV diversi cation. Despite these efforts, and lack of extensive sampling, there is limited knowledge about the MSV-A diversity in Ethiopia. Here, eld 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 725 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 elds 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 newly determined MSV isolates belong in the recombinant lineage V of the A 1 subtype with the widest dissemination, and economic signi cance in the sub-Saharan Africa and the adjacent Indian Ocean islands. Main TextMaize streak virus strain A (MSV-A) (species Maize streak virus; genus Mastrevirus, family Geminiviridae) is the causal agent of maize streak disease (MSD) in maize plant. In sub-Saharan Africa this disease is of economic importance to large, small, and subsistence scale farmers, because in epidemic years the infection by the virus can cause complete yield loss [1][2][3]. Infected maize plants display characteristic chlorotic streaks on their leaves, are severely stunted, have low yields and occasionally die [4][5][6]. The epidemiology and spread of MSV-A is complex and is strongly dependent on the behaviours and population dynamics of the leafhopper species Cicadulina sp. that transmits it. [2,[7][8][9].