Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya
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...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Springer
2018
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| Online Access: | https://hdl.handle.net/10568/93430 |
| _version_ | 1855540939913691136 |
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| author | Wamaitha, M. Jane Nigam, Deepti Maina, Solomon Stomeo, Francesca Wangai, Anne Njuguna, Joyce N. Holton, Timothy A. Wanjala, Bramwel W. Wamalwa, Mark Lucas, Tanui Djikeng, Appolinaire García Ruiz, H. |
| author_browse | Djikeng, Appolinaire García Ruiz, H. Holton, Timothy A. Lucas, Tanui Maina, Solomon Nigam, Deepti Njuguna, Joyce N. Stomeo, Francesca Wamaitha, M. Jane Wamalwa, Mark Wangai, Anne Wanjala, Bramwel W. |
| author_facet | Wamaitha, M. Jane Nigam, Deepti Maina, Solomon Stomeo, Francesca Wangai, Anne Njuguna, Joyce N. Holton, Timothy A. Wanjala, Bramwel W. Wamalwa, Mark Lucas, Tanui Djikeng, Appolinaire García Ruiz, H. |
| author_sort | Wamaitha, M. Jane |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. 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. 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. 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. |
| format | Journal Article |
| id | CGSpace93430 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace934302024-10-03T07:41:01Z Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya Wamaitha, M. Jane Nigam, Deepti Maina, Solomon Stomeo, Francesca Wangai, Anne Njuguna, Joyce N. Holton, Timothy A. Wanjala, Bramwel W. Wamalwa, Mark Lucas, Tanui Djikeng, Appolinaire García Ruiz, H. maize viruses research 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. 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. 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. 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. 2018-12 2018-06-25T08:36:31Z 2018-06-25T08:36:31Z Journal Article https://hdl.handle.net/10568/93430 en Open Access Springer Wamaitha, M.J., Nigam, D., Maina, S., Stomeo, F., Wangai, A., Njuguna, J.N., Holton, T.A., Wanjala, B.W., Wamalwa, M., Lucas, T., Djikeng, A. and Garcia-Ruiz, H. 2018. Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya. Virology Journal 15: 90 |
| spellingShingle | maize viruses research Wamaitha, M. Jane Nigam, Deepti Maina, Solomon Stomeo, Francesca Wangai, Anne Njuguna, Joyce N. Holton, Timothy A. Wanjala, Bramwel W. Wamalwa, Mark Lucas, Tanui Djikeng, Appolinaire García Ruiz, H. Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title | Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title_full | Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title_fullStr | Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title_full_unstemmed | Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title_short | Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya |
| title_sort | metagenomic analysis of viruses associated with maize lethal necrosis in kenya |
| topic | maize viruses research |
| url | https://hdl.handle.net/10568/93430 |
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