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Open Access 01-12-2018 | Research

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

Authors: Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A. Holton, Bramwel W. Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia-Ruiz

Published in: Virology Journal | Issue 1/2018

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.

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Title: Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya
Authors: Mwathi Jane Wamaitha
Deepti Nigam
Solomon Maina
Francesca Stomeo
Anne Wangai
Joyce Njoki Njuguna
Timothy A. Holton
Bramwel W. Wanjala
Mark Wamalwa
Tanui Lucas
Appolinaire Djikeng
Hernan Garcia-Ruiz
Publication date: 01-12-2018
Publisher: BioMed Central
Published in: Virology Journal / Issue 1/2018
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-018-0999-2

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Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

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