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Extensive recombination challenges the utility of Sugarcane mosaic virus phylogeny and strain typing.

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Braidwood, Luke 
Müller, Sebastian Y  ORCID logo


Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.



Genes, Viral, High-Throughput Nucleotide Sequencing, Phylogeny, Potyvirus, Recombination, Genetic, Saccharum, Species Specificity

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Springer Science and Business Media LLC


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European Research Council (340642)
The authors would like to acknowledge colleagues at KALRO for their assistance in maize sampling, to farmers in all study areas for providing maize samples, and to John Welch for guidance on phylogenetic analyses. L.B. is supported by the BBSRC DTP and the 2Blades Foundation, S.Y.M. was supported by the European Research Council Advanced Investigator Grant ERC-2013-AdG 340642 - TRIBE and D.C.B. is supported by the Royal Society Edward Penley Abraham Research Professorship.