Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

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

doi:10.1186/s12985-018-0999-2

Abstract

BackgroundMaize 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.MethodsWe 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.ResultsComplete 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.ConclusionOur 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.

Highlights

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)
Identification of maize-infecting viruses To gain insight on viruses associated with maize lethal necrosis and their genetic variation in Kenya, we conducted a metagenomics analysis based on nextgeneration RNA sequencing, de-novo assembly and identification of viruses in Kenya (Fig. 1b) through bioinformatics
Results clearly indicated the presence of four main viruses: Maize chlorotic mottle virus (MCMV), Sugarcane mosaic virus (SCMV), Maize streak virus (MSV) and Maize Yellow Dwarf virus-RMV (MYDV-RMV) (Fig. 1c)

Summary

Introduction

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). In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. In 2011 maize lethal necrosis disease was first detected in Kenya [5,6,7], and confirmed in several countries in East and Central Africa, in Tanzania, Uganda [8], Rwanda [9] DR Congo [10], Ethiopia and South Sudan [11]. Corn lethal necrosis (CLN) was first described in the State of Kansas in 1978 [12]. In their original descriptions, corn lethal necrosis and maize lethal necrosis defined the same disease.

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Conclusion