TY - JOUR
T1 - Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya
AU - Wamaitha, Mwathi Jane
AU - Nigam, Deepti
AU - Maina, Solomon
AU - Stomeo, Francesca
AU - Wangai, Anne
AU - Njuguna, Joyce Njoki
AU - Holton, Timothy A.
AU - Wanjala, Bramwel W.
AU - Wamalwa, Mark
AU - Lucas, Tanui
AU - Djikeng, Appolinaire
AU - Garcia-Ruiz, Hernan
N1 - Funding Information:
We thank the Director General KALRO for spearheading the Research and supporting study leave for Mwathi Jane Wamaitha, and Dr. Rob Skilton for guidance. The Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, for Next generation sequencing. Mwathi Jane Wamaitha was the recipient of a Borlaug International Agricultural Science and Technology fellowship (2017) from the USDA Foreign Agricultural Service. The bioinformatics work was completed, through HGR lab, at the Holland Computing Center of the University of Nebraska-Lincoln, which receives support from the Nebraska Research Initiative.
Funding Information:
Sampling was supported by the Government of Kenya (GoK) through a competitive World Bank Supported program, Kenya Agricultural Productivity and Agribusiness collaborative research Project (KAPAP-CGS Grant (2014–2015) through Kenya Agricultural and Livestock Research Organization (KALRO) as the lead organization, collaborating with Ministry of Agriculture, Livestock and Fisheries-PPSD, KELPHIS, PCPB, ICIPE and University of Nairobi. The NGS was supported by BecA-ILRI Hub through the Africa Biosciences Challenge Fund (ABCF) program. The ABCF Program is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and the Swedish International Development Cooperation Agency (SIDA). The Bioinformatics analysis was supported by Borlaug International Agricultural Science and Technology fellowship (2017) from the USDA Foreign Agricultural Service to MJW hosted by the HGR lab. HGR lab is supported by NIH grant RO1GM120108 and by the Nebraska Agricultural Experiment Station with funding from the Hatch Act (Accession Number 1007272) through the USDA National Institute of Food and Agriculture.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/5/23
Y1 - 2018/5/23
N2 - 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.
AB - 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.
KW - Coat protein variation
KW - MCMV
KW - MSV
KW - MYDV-RMV
KW - Maize lethal necrosis
KW - Metagenomics
KW - Phylogenetics
KW - SCMV
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U2 - 10.1186/s12985-018-0999-2
DO - 10.1186/s12985-018-0999-2
M3 - Article
C2 - 29792207
AN - SCOPUS:85047621217
SN - 1743-422X
VL - 15
JO - Virology Journal
JF - Virology Journal
IS - 1
M1 - 90
ER -