Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya
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RESEARCH
Open Access
Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya Mwathi Jane Wamaitha1*, Deepti Nigam2, Solomon Maina3,4, Francesca Stomeo5, Anne Wangai1, Joyce Njoki Njuguna5, Timothy A. Holton6, Bramwel W. Wanjala5, Mark Wamalwa5, Tanui Lucas1, Appolinaire Djikeng5,7 and Hernan Garcia-Ruiz2*
Abstract Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples were collected from maize and sorghum representing sixteen counties. Results: Complete and partial genomes were assembled for MCMV, SCMV, Maize streak virus (MSV) and Maize yellow dwarf virus-RMV (MYDV-RMV). These four viruses (MCMV, SCMV, MSV and MYDV-RMV) were found together in 30 of 68 samples. A geographic analysis showed that these viruses are widely distributed in Kenya. Phylogenetic analyses of nucleotide sequences showed that MCMV, MYDV-RMV and MSV are similar to isolates from East Africa and other parts of the world. Single nucleotide polymorphism, nucleotide and polyprotein sequence alignments identified three genetically distinct groups of SCMV in Kenya. Variation mapped to sequences at the border of NIb and the coat protein. Partial genome sequences were obtained for other four potyviruses and one polerovirus. Conclusion: Our results uncover the complexity of the maize lethal necrosis epidemic in Kenya. MCMV, SCMV, MSV and MYDV-RMV are widely distributed and infect both maize and sorghum. SCMV population in Kenya is diverse and consists of numerous strains that are genetically different to isolates from other parts of the world. Several potyviruses, and possibly poleroviruses, are also involved. Keywords: Maize lethal necrosis, MCMV, SCMV, MYDV-RMV, MSV, Metagenomics, Phylogenetics, Coat protein variation
Background Maize (Zea mays L.) is one of the most important cereals in Sub-Saharan Africa and is grown in approximately 25 million hectares [1]. Maize is consumed as a preferred calorie source by 95% of the population, at an average of 1075 kcal/capita/day, which represents more than 50% of the recommended daily * Correspondence: [email protected]; [email protected] 1 Kenya Agricultural and Livestock Research Organization (KALRO), P. O. Box 14733-00800, Nairobi, Kenya 2 Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska- Lincoln, Lincoln, NE 68583, USA Full list of author information is available at the end of the article
intake [2]. Maize production is de
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