Reconstructing the history of Maize streak virus 1 strain-A dispersal to reveal diversification 2 hotspots and its origin in southern Africa 3 4

64 65 Maize streak virus (MSV) strain A, the causal agent of Maize streak disease is 66 today one of the most serious biotic threats to African food security. Determining 67 where MSV-A originated and how it spread trans-continentally could yield 68 valuable insights into its historical emergence as a crop pathogen. Similarly, 69 determining where the major extant MSV-A lineages arose could identify 70 geographical hotspots of MSV evolution. Here, we use model-based 71 phylogeographic analyses of 353 fully-sequenced MSV-A isolates to reconstruct 72 a plausible history of MSV-A movements over the past 150 years. We show that 73 since the probable emergence of MSV-A in southern Africa around 1863, the 74 virus spread trans-continentally at an average rate of 32.5 km/yr (95% highest 75 probability density intervals 15.6-51.6 km/yr). Using distinctive patterns of 76 nucleotide variation caused by 20 unique intra-MSV-A recombination events we 77 tentatively classified the MSV-A isolates into 24 easily discernable lineages. 78 Despite many of these lineages displaying distinct geographical distributions, it is 79 apparent that almost all have emerged within the past four decades from either 80 southern or eastern-central Africa. Collectively, our results suggest that regular 81 analysis of MSV-A genomes within these diversification hotspots could be used 82 to monitor the emergence of future MSV-A lineages that could affect maize 83 cultivation in Africa. 84 85 on O cber 2, 2017 by gest http/jvi.asm .rg/ D ow nladed fom