title: The role of Kenya in the trans-African spread of maize streak virus strain A.
abstract: Maize streak virus (MSV), the causal agent of maize streak disease (MSD), is the most important viral pathogen of Africa's staple food crop, maize. Previous phylogeographic analyses have revealed that the most widely-distributed and common MSV variant, MSV-A1, has been repeatedly traversing Africa over the past fifty years with long-range movements departing from either the Lake Victoria region of East Africa, or the region around the convergence of Zimbabwe, South Africa and Mozambique in southern Africa. Despite Kenya being the second most important maize producing country in East Africa, little is known about the Kenyan MSV population and its contribution to the ongoing diversification and trans-continental dissemination of MSV-A1. We therefore undertook a sampling survey in this country between 2008 and 2011, collecting MSD prevalence data in 119 farmers' fields, symptom severity data for 170 maize plants and complete MSV genome sequence data for 159 MSV isolates. We then used phylogenetic and phylogeographic analyses to show that whereas the Kenyan MSV population is likely primarily derived from the MSV population in neighbouring Uganda, it displays considerably more geographical structure than the Ugandan population. Further, this geographical structure likely confounds apparent associations between virus genotypes and both symptom severity and MSD prevalence in Kenya. Finally, we find that Kenya is probably a sink rather than a source of MSV diversification and movement, and therefore, unlike Uganda, Kenya probably does not play a major role in the trans-continental dissemination of MSV-A1.
authors.affiliation: Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya; Biological and Biomedical Science and Technology, Laikipia University, P.O. Box 1100-20300, Nyahururu, Kenya.
authors.forename: Daniel
authors.initials: D
authors.lastname: Pande
authors.affiliation: South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa.
authors.forename: Eugene
authors.initials: E
authors.lastname: Madzokere
authors.affiliation: Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa.
authors.forename: Penelope
authors.initials: P
authors.lastname: Hartnady
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: Simona
authors.initials: S
authors.lastname: Kraberger
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
authors.forename: James
authors.initials: J
authors.lastname: Hadfield
authors.affiliation: College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
authors.forename: Karyna
authors.initials: K
authors.lastname: Rosario
authors.affiliation: School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; Department of Infectious Diseases, University of Heidelberg, D-69120 Heidelberg, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Jäschke
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa; Department of Immunology, Norwegian Veterinary Institute, Pb 750 Sentrum, N-0106 Oslo, Norway.
authors.forename: Adérito L
authors.initials: AL
authors.lastname: Monjane
authors.affiliation: Department of Agricultural Production, School of Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda.
authors.forename: Betty E
authors.initials: BE
authors.lastname: Owor
authors.affiliation: Department of Applied Plant Sciences, School of Agriculture and Food Security, Maseno, Kenya.
authors.forename: Mathews M
authors.initials: MM
authors.lastname: Dida
authors.affiliation: Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa.
authors.forename: Dionne N
authors.initials: DN
authors.lastname: Shepherd
authors.affiliation: Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7001, South Africa; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA. Electronic address: arvind.varsani@asu.edu.
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
authors.affiliation: South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa. Electronic address: gordon@sanbi.ac.za.
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Harkins
mesh_terms: D004279:DNA, Viral / Q000235:genetics*; D016679:Genome, Viral; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D007630:Kenya; D026762:Maize streak virus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography; D010935:Plant Diseases / Q000821:virology*; D014454:Uganda; D003313:Zea mays / Q000821:virology*
chemical_list: D004279:DNA, Viral
keywords: Geminivirus; Kenya; MSV spread; Maize streak virus; Mastrevirus