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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Use of next-generation sequencing for the identification and characterization of maize chlorotic mottle virus and sugarcane mosaic virus causing maize lethal necrosis in kenya
Plant Pathology, Volume 62, No. 4, Year 2013
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Description
The diagnosis of novel unidentified viral plant diseases can be problematic, as the conventional methods such as real-time PCR or ELISA may be too specific to a particular species or even strain of a virus, whilst alternatives such as electron microscopy (EM) or sap inoculation of indicator species do not usually give species level diagnosis. Next-generation sequencing (NGS) offers an alternative solution where sequence is generated in a non-specific fashion and identification is based on similarity searching against GenBank. The conventional and NGS techniques were applied to a damaging and apparently new disease of maize, which was first identified in Kenya in 2011. ELISA and TEM provided negative results, whilst inoculation of other cereal species identified the presence of an unidentified sap transmissible virus. RNA was purified from material showing symptoms and sequenced using a Roche 454 GS-FLX+. Database searching of the resulting sequence identified the presence of Maize chlorotic mottle virus and Sugarcane mosaic virus, a combination previously reported to cause maize lethal necrosis disease. Over 90% of both viral genome sequences were obtained, allowing strain characterization and the development of specific real-time PCR assays which were used to confirm the presence of the virus in material with symptoms from six different fields in two different regions of Kenya. The availability of these assays should aid the assessment of the disease and may be used for routine diagnosis. The work shows that next-generation sequencing is a valuable investigational technique for rapidly identifying potential disease-causing agents such as viruses. © 2012 The Authors Plant Pathology © 2012 BSPP.
Authors & Co-Authors
Adams, Ian Patrick
United Kingdom, York
Fera Science Limited
Miano, Douglas Watuku
Kenya, Nairobi
Kenya Agricultural Research Institute
Kinyua, Zakary M.
Kenya, Nairobi
Kenya Agricultural Research Institute
Wangai, Anne W.
Kenya, Nairobi
Kenya Agricultural Research Institute
Kimani, Esther N.
Kenya, Nairobi
Kenya Plant Health Inspectorate Service
Phiri, Noah A.
Kenya, Nairobi
Cabi, Kenya
Reeder, Robert H.
United Kingdom, Egham
Cab International
Harju, Valerie A.
United Kingdom, York
Fera Science Limited
Glover, Rachel H.
United Kingdom, York
Fera Science Limited
Hany, Ummey
United Kingdom, York
Fera Science Limited
Souza-Richards, Rose
United Kingdom, York
Fera Science Limited
United Kingdom, Nottingham
University of Nottingham
Deb Nath, P.
United Kingdom, York
Fera Science Limited
India, Jorbat
Assam Agricultural University
Nixon, T.
United Kingdom, York
Fera Science Limited
Fox, Adrian
United Kingdom, York
Fera Science Limited
Barnes, A. V.
United Kingdom, York
Fera Science Limited
Smith, Julian J.
United Kingdom, York
Fera Science Limited
Skelton, Anna L.
United Kingdom, York
Fera Science Limited
Thwaites, Richard M.
United Kingdom, York
Fera Science Limited
Mumford, Rick
United Kingdom, York
Fera Science Limited
Boonham, Neil
United Kingdom, York
Fera Science Limited
Statistics
Citations: 91
Authors: 20
Affiliations: 7
Identifiers
Doi:
10.1111/j.1365-3059.2012.02690.x
ISSN:
00320862
e-ISSN:
13653059
Study Locations
Kenya