Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya

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

Research output: Contribution to journalArticle

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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.

Original languageEnglish (US)
Article number90
JournalVirology Journal
Volume15
Issue number1
DOIs
StatePublished - May 23 2018

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Metagenomics
Kenya
Zea mays
Necrosis
Mosaic Viruses
Viruses
Saccharum
Maize streak virus
Luteoviridae
Potyvirus
Sorghum
Potyviridae
Genome
Polyproteins
Eastern Africa
Sequence Alignment
Capsid Proteins
Poaceae
Coinfection

Keywords

  • Coat protein variation
  • MCMV
  • MSV
  • MYDV-RMV
  • Maize lethal necrosis
  • Metagenomics
  • Phylogenetics
  • SCMV

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya. / Wamaitha, Mwathi Jane; Nigam, Deepti; Maina, Solomon; Stomeo, Francesca; Wangai, Anne; Njuguna, Joyce Njoki; Holton, Timothy A.; Wanjala, Bramwel W.; Wamalwa, Mark; Lucas, Tanui; Djikeng, Appolinaire; Garcia Ruiz, Hernan.

In: Virology Journal, Vol. 15, No. 1, 90, 23.05.2018.

Research output: Contribution to journalArticle

Wamaitha, MJ, Nigam, D, Maina, S, Stomeo, F, Wangai, A, Njuguna, JN, Holton, TA, Wanjala, BW, Wamalwa, M, Lucas, T, Djikeng, A & Garcia Ruiz, H 2018, 'Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya', Virology Journal, vol. 15, no. 1, 90. https://doi.org/10.1186/s12985-018-0999-2
Wamaitha MJ, Nigam D, Maina S, Stomeo F, Wangai A, Njuguna JN et al. Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya. Virology Journal. 2018 May 23;15(1). 90. https://doi.org/10.1186/s12985-018-0999-2
Wamaitha, Mwathi Jane ; Nigam, Deepti ; Maina, Solomon ; Stomeo, Francesca ; Wangai, Anne ; Njuguna, Joyce Njoki ; Holton, Timothy A. ; Wanjala, Bramwel W. ; Wamalwa, Mark ; Lucas, Tanui ; Djikeng, Appolinaire ; Garcia Ruiz, Hernan. / Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya. In: Virology Journal. 2018 ; Vol. 15, No. 1.
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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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AU - Njuguna, Joyce Njoki

AU - Holton, Timothy A.

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